/**
 * Get_terms()で、特定の投稿タイプのみcountの対象にする
 *
 * @param object $clauses clauses.
 * @param string $taxonomy taxonomy.
 * @param object $args args.
 * @return object $clauses clauses.
 */
function get_terms_posttype($clauses, $taxonomy, $args) {
    if (!empty($args['post_type']))    {
        global $wpdb;
        $post_types = array();
        if( $args['post_type'] ){
            foreach($args['post_type'] as $cpt)    {
                $post_types[] = "'".$cpt."'";
            }
        }
        if(!empty($post_types))    {
            $clauses['fields'] = 'DISTINCT '.str_replace('tt.*', 'tt.term_taxonomy_id, tt.term_id, tt.taxonomy, tt.description, tt.parent', $clauses['fields']).', COUNT(t.term_id) AS count';
            $clauses['join'] .= ' INNER JOIN '.$wpdb->term_relationships.' AS r ON r.term_taxonomy_id = tt.term_taxonomy_id INNER JOIN '.$wpdb->posts.' AS p ON p.ID = r.object_id';
            $clauses['where'] .= ' AND p.post_status = "publish" AND p.post_type IN ('.implode(',', $post_types).')';
            $clauses['orderby'] = 'GROUP BY t.term_id '.$clauses['orderby'];
        }
    }
//     print_r($clauses);exit;
    return $clauses;
}
add_filter('terms_clauses', 'get_terms_posttype', 10, 3);

$taxonomies = array( 'タクソノミー名' );
$post_type  = array( '投稿タイプ名' );
$args       = array(
    'taxonomy'   => $taxonomies,
    'post_type'  => $post_type  ,
    'orderby'    => 'menu_order',
    'order'      => 'ASC',
    'hide_empty' => true,
);
$terms      = get_terms( $args );