parse_tax_query causing Navigation Menu To Disappear

Query parsing happens on every query run on a page, not just the main query. Your parse_tax_query is modifying the query for menu items in your menu. Check is_main_query() to make sure you only change the main query:

function no_child_terms($query) {
    if( !is_admin() && $query->is_main_query() ){
        $query->tax_query->queries[0]['include_children'] = 0;
    }
}
add_action('parse_tax_query', 'no_child_terms');