Perhaps a bit quick and dirty, but this should work:
function media_library_hide_dlm_downloads($where) {
if(isset($_POST['action']) && ( $_POST['action'] == 'query-attachments')) {
$where .= ' AND guid NOT LIKE "%wp-content/uploads/dlm_downloads%"';
}
return $where;
}
add_filter('posts_where', 'media_library_hide_dlm_downloads');
Read more about the posts_where filter.