This is mostly pure PHP, but you need to implode
the array.
add_shortcode('bundled_ids','bundled_ids_func');
function bundled_ids_func() {
$meta_values = get_post_meta( get_the_ID() , '_bundled_ids', true );
if (!empty($meta_values)) {
$mydata = implode(',',$meta_values); // add this line
return $mydata;
}
}