WordPress Menu Disappears when $query->query_vars[‘meta_key’] is set

Nav menus are also generated by a WP_Query, so in your pre_get_posts callback function you need to check if the $query you’re altering is the main query. The easiest way to do this would probably be to do this right at the beginning of the function:

if ( ! $query->is_main_query() )
    return $query;

Also note that in your jh_popularity_sort_query() callback function, you should probably use the set() method instead, e.g. $query->set( 'orderby', 'date' ). The method does exactly what you’re doing above with changing the $query_vars array, but it’ll keep you safer going forward. I think it also makes for slightly prettier code 🙂