Alrighty, I think I've got it.

MAKE A BACKUP BEFORE YOU MAKE THIS CHANGE BECAUSE THIS ISN'T AN OVERRIDE FILE and it worked for me, but I'm not 100% sure it is correct.

In includes/modules/pages/advanced_search_result/header.php, find
PHP Code:
$from_str "FROM (" TABLE_PRODUCTS " p
             LEFT JOIN " 
TABLE_MANUFACTURERS " m
             USING(manufacturers_id), " 
TABLE_PRODUCTS_DESCRIPTION " pd, " TABLE_CATEGORIES " c, " TABLE_PRODUCTS_TO_CATEGORIES " p2c )
             LEFT JOIN " 
TABLE_META_TAGS_PRODUCTS_DESCRIPTION " mtpd
             ON mtpd.products_id= p2c.products_id
             AND mtpd.language_id = :languagesID"

and change to
PHP Code:
$from_str "FROM (" TABLE_HIDE_CATEGORIES " h, " TABLE_PRODUCTS " p
             LEFT JOIN " 
TABLE_MANUFACTURERS " m
             USING(manufacturers_id), " 
TABLE_PRODUCTS_DESCRIPTION " pd, " TABLE_CATEGORIES " c, " TABLE_PRODUCTS_TO_CATEGORIES " p2c )
             LEFT JOIN " 
TABLE_META_TAGS_PRODUCTS_DESCRIPTION " mtpd
             ON mtpd.products_id= p2c.products_id
             AND mtpd.language_id = :languagesID"

Then find
PHP Code:
// Notifier Point
$zco_notifier->notify('NOTIFY_SEARCH_FROM_STRING');

$where_str " WHERE (p.products_quantity > 0
               AND p.products_status = 1
               AND p.products_id = pd.products_id
               AND pd.language_id = :languagesID
               AND p.products_id = p2c.products_id
               AND p2c.categories_id = c.categories_id "

and change to
PHP Code:
// Notifier Point
$zco_notifier->notify('NOTIFY_SEARCH_FROM_STRING');

$where_str " WHERE (p.products_quantity > 0
               AND p.products_status = 1
               AND p.products_id = pd.products_id
               AND pd.language_id = :languagesID
               AND p.products_id = p2c.products_id
               and (p.master_categories_id = h.categories_id and h.visibility_status !=2)
               AND p2c.categories_id = c.categories_id "

All I did was utilize the code from hideCategories/includes/modules/sideboxes/my_template/whats_new.php and adapted it to fit the search code.

Hopefully it will continue to work and not cause issues with any of my other mods but I would appreciate feedback from someone who knows code as to whether it is the appropriate way to handle this situation.

Thanks!