Looking at the header, it seems you can either create your own WordPress menu for the secondary-menu, or a “woo_custom_navigation” menu. If any of these are set (and maybe they can even be empty), the category list will not be displayed.
You could also create a child theme, with only the header.php file. This would be a copy of the header.php file of the Bueno theme with the relevant lines removed.
<?php
if ( function_exists('has_nav_menu') && has_nav_menu('secondary-menu') ) {
wp_nav_menu( array( 'sort_column' => 'menu_order', 'container' => 'ul', 'menu_id' => 'catnav', 'menu_class' => 'nav fl', 'theme_location' => 'secondary-menu' ) );
} else {
?>
<ul id="catnav" class="nav fl">
<?php
if ( get_option('woo_custom_nav_menu') == 'true' ) {
if ( function_exists('woo_custom_navigation_output') )
woo_custom_navigation_output('name=Woo Menu 2');
} else { ?>
<?php wp_list_categories('sort_column=menu_order&depth=3&title_li=&exclude=".get_option("woo_nav_exclude')); ?>
<?php } ?>
</ul><!-- /#nav -->
<?php } ?>