How loop through posts based on custom fields

To select posts that have a meta value, use the EXISTS comparison operator.

$args = array(
    'post_type' => 'jobs',
    'posts_per_page' => 12,
    'paged'=> $paged,
    'tax_query' => array(
        array(
            'taxonomy' => 'job_category',
            'field'    => 'slug',
            'terms'    => $term->slug,
        )
    ),
    'meta_query' => array(
        array(
            'key'     => '_shop',
            'compare' => 'EXISTS'
        )
    )
);