in_category() and tax_query with custom post type

Instead of in_category try has_term – http://codex.wordpress.org/Function_Reference/has_term

This should work (I’ve tested it in a simpler form on my localhost):

<?php get_header(); ?>

    <div id="body">
    <div class="fix">
    <?php if (have_posts()) : while (have_posts()) : the_post(); ?>


    <?php   
    if ( has_term('natige', 'products_brand')) :?>
        <div class="col-2 nati-col">
        <div class="col-left">
            <div class="nav">
            <a href="https://wordpress.stackexchange.com/questions/137042/<?php 
            if (ICL_LANGUAGE_CODE =="ru'){
                echo "/ru/produkciya-natizhe";
            } elseif (ICL_LANGUAGE_CODE == 'kz'){  
                echo "/natizhe-onimi";
            }
            ?>" class="natiact"><?php _e( 'Продукция «Н&#1241;тиже»', 'wpml_theme');?></a>
            <a href="https://wordpress.stackexchange.com/questions/137042/<?php 
            if (ICL_LANGUAGE_CODE =="ru'){
                echo "/ru/produkciya-osakarovka";
            } elseif (ICL_LANGUAGE_CODE == 'kz'){  
                echo "/osakarovka-onimi";
            }
            ?>" class="osahover"><?php _e( 'Продукция «Осакаровка»', 'wpml_theme');?></a>
            </div>

    <div class="product-under">
    <div class="pu-left"><?php the_post_thumbnail( 'product-page' ); ?>

    <?php
    if( get_field('dop_izobrazheniye') ): ?>
    <img style="margin-top: 60px;" alt="<?php the_title_attribute(); ?>" title="<?php the_title_attribute(); ?>" src="<?php $image = get_field('dop_izobrazheniye'); echo($image['sizes']['product-page']); ?>"/>
    <?php endif; ?>
    </div>
    <div class="pu-right"><h1><?php the_title(); ?></h1>

                    <?php if( get_field('product_parameter') ): ?>

                        <?php while( has_sub_field('product_parameter') ): ?>

                                <?php if( get_sub_field('pack_volume_fat') ): ?>
                                    <?php while( has_sub_field('pack_volume_fat') ): ?>
                                    <ul class="prodparam">

                                        <li><b><?php the_sub_field('pack'); ?></b></li>
                                        <?php if (get_sub_field('mass_fat') ): ?>
                                            <li><?php while( has_sub_field('mass_fat') ): ?>

                                            <?php the_sub_field('mass'); ?>
                                            <?php the_sub_field('measure'); ?>&nbsp;&mdash;&nbsp;
                                            <?php the_sub_field('fatness'); ?></li>

                                            <?php endwhile; ?>
                                        <?php endif; ?>
                                    </ul>
                                    <?php endwhile; ?>

                                <?php endif; ?>

                        <?php endwhile; ?>

                    <?php endif; ?>

                <?php the_content(); ?>


    </div>
                <?php wp_reset_query(); ?>
    <div class="clear"></div>
    </div>

    <hr><br>

    <?php $orig_post = $post;
        global $post;
        $tags = wp_get_post_tags($post->ID);
        if ($tags) {
        $tag_ids = array();
        foreach($tags as $individual_tag) $tag_ids[] = $individual_tag->term_id;
        $args=array(
        'tag__in' => $tag_ids,
        'post__not_in' => array($post->ID),
        'post_type' => 'products',
        'posts_per_page'=>6, // Number of related posts that will be shown.
        'caller_get_posts'=>1
        );
        $my_query = new wp_query( $args );
        if( $my_query->have_posts() ) {


        echo _e( '<h2>Рекомендуем посмотреть</h2>', 'wpml_theme');

    echo '<ul class="products">';
        while( $my_query->have_posts() ) {
        $my_query->the_post(); ?>

        <li>
            <a href="<?php the_permalink(); ?>" title="<?php the_title_attribute(); ?>" alt="<?php the_title_attribute(); ?>"><i><?php the_post_thumbnail( 'product-cat' ); ?></i><?php the_title(); ?></a>
        </li>
        <? }
        }
        }
        $post = $orig_post;
        wp_reset_query(); ?>
        </ul>
        </div>
        <div class="col-right">
            <ul class="product-list">
            <?php $pc = new WP_Query(array(
            'order' => 'ASC', 
            'orderby' => 'title', 
            'posts_per_page' => '45', 
            'post_type' => 'products',
            'tax_query' => array(
                        array(
                        'taxonomy' => 'products_brand',
                        'field' => 'slug',
                        'terms' => 'natige'
                    )
                )
            ));

            ?>
                <?php while ($pc->have_posts()) : $pc->the_post(); ?>
                <li>
                <a href="<?php the_permalink(); ?>" title="<?php the_title_attribute(); ?>"><?php the_title(); ?></a>
                </li>
            <?php endwhile; ?>
            <?php wp_reset_query() ?>
            </ul>
        </div>
        <div class="clear"></div>
    </div>







    <?php elseif ( has_term('osakarovka', 'products_brand')) :?>
        <div class="col-2 osakarov-col">
        <div class="col-left">
            <div class="nav">
            <a href="https://wordpress.stackexchange.com/questions/137042/<?php 
            if (ICL_LANGUAGE_CODE =="ru'){
                echo "/ru/produkciya-natizhe";
            } elseif (ICL_LANGUAGE_CODE == 'kz'){  
                echo "/natizhe-onimi";
            }
            ?>" class="natihover"><?php _e( 'Продукция «Н&#1241;тиже»', 'wpml_theme');?></a>
            <a href="https://wordpress.stackexchange.com/questions/137042/<?php 
            if (ICL_LANGUAGE_CODE =="ru'){
                echo "/ru/produkciya-osakarovka";
            } elseif (ICL_LANGUAGE_CODE == 'kz'){  
                echo "/osakarovka-onimi";
            }
            ?>" class="osaact"><?php _e( 'Продукция «Осакаровка»', 'wpml_theme');?></a>
            </div>

    <div class="product-under">
    <div class="pu-left"><?php the_post_thumbnail( 'product-page' ); ?>

    <?php
    if( get_field('dop_izobrazheniye') ): ?>
    <img style="margin-top: 60px;" alt="<?php the_title_attribute(); ?>" title="<?php the_title_attribute(); ?>" src="<?php $image = get_field('dop_izobrazheniye'); echo($image['sizes']['product-page']); ?>"/>
    <?php endif; ?>
    </div>
    <div class="pu-right"><h1 class="osak-prod"><?php the_title(); ?></h1>

                    <?php if( get_field('product_parameter') ): ?>

                        <?php while( has_sub_field('product_parameter') ): ?>

                                <?php if( get_sub_field('pack_volume_fat') ): ?>
                                    <?php while( has_sub_field('pack_volume_fat') ): ?>
                                    <ul class="prodparam">

                                        <li><b><?php the_sub_field('pack'); ?></b></li>
                                        <?php if (get_sub_field('mass_fat') ): ?>
                                            <li><?php while( has_sub_field('mass_fat') ): ?>

                                            <?php the_sub_field('mass'); ?>
                                            <?php the_sub_field('measure'); ?>&nbsp;&mdash;&nbsp;
                                            <?php the_sub_field('fatness'); ?></li>

                                            <?php endwhile; ?>
                                        <?php endif; ?>
                                    </ul>
                                    <?php endwhile; ?>

                                <?php endif; ?>

                        <?php endwhile; ?>

                    <?php endif; ?>

                <?php the_content(); ?>


    </div>
                <?php wp_reset_query(); ?>
    <div class="clear"></div>
    </div>

    <hr><br>

    <?php $orig_post = $post;
        global $post;
        $tags = wp_get_post_tags($post->ID);
        if ($tags) {
        $tag_ids = array();
        foreach($tags as $individual_tag) $tag_ids[] = $individual_tag->term_id;
        $args=array(
        'tag__in' => $tag_ids,
        'post__not_in' => array($post->ID),
        'post_type' => 'products',
        'posts_per_page'=>6, // Number of related posts that will be shown.
        'caller_get_posts'=>1
        );
        $my_query = new wp_query( $args );
        if( $my_query->have_posts() ) {


        echo _e( '<h2>Рекомендуем посмотреть</h2>', 'wpml_theme');

    echo '<ul class="products">';
        while( $my_query->have_posts() ) {
        $my_query->the_post(); ?>

        <li>
            <a href="<?php the_permalink(); ?>" title="<?php the_title_attribute(); ?>" alt="<?php the_title_attribute(); ?>"><i><?php the_post_thumbnail( 'product-cat' ); ?></i><?php the_title(); ?></a>
        </li>
        <? }
        }
        }
        $post = $orig_post;
        wp_reset_query(); ?>
        </ul>
        </div>
        <div class="col-right">
            <ul class="product-list">
            <?php $pc = new WP_Query(array(
            'order' => 'ASC', 
            'orderby' => 'title', 
            'posts_per_page' => '45', 
            'post_type' => 'products',
            'tax_query' => array(
                        array(
                        'taxonomy' => 'products_brand',
                        'field' => 'slug',
                        'terms' => 'osakarovka'
                    )
                )
            ));

            ?>
                <?php while ($pc->have_posts()) : $pc->the_post(); ?>
                <li>
                <a href="<?php the_permalink(); ?>" title="<?php the_title_attribute(); ?>"><?php the_title(); ?></a>
                </li>
            <?php endwhile; ?>
            <?php wp_reset_query() ?>
            </ul>
        </div>
        <div class="clear"></div>
    </div>

    <?php endif;  ?>

    <?php endwhile; else : ?>
    <?php endif; ?>




    </div>

    </div>


    <?php get_footer(); ?>