Для этого в файле /core/functions/category_funtions.php заменить:
$q = db_query( "select categoryID, parent, name, products_count, uri from ".CATEGORIES_TABLE. " where parent=1 ". " order by sort_order, name " );на
$q = db_query( "select categoryID, parent, name, products_count, uri from ".CATEGORIES_TABLE. " where parent=1 AND sort_order!=1000 ". " order by sort_order, name " );