I just try this code in my functions.php to see if it have any effects on taxonomy field without any result ? That very strange. Or I do not do it correctly.
add_filter('acf/fields/taxonomy/query', 'my_acf_fields_taxonomy_query', 10, 3);
function my_acf_fields_taxonomy_query( $args, $field, $post_id ) {
// Show 40 terms per AJAX call.
$args['number'] = 40;
// Order by most used.
$args['orderby'] = 'count';
$args['order'] = 'DESC';
return $args;
}