Didn't used btrfs with PVE yet. But as far as I know, a directroy storage won't make any use of the features of the underlaying storage. The documentation lists that a btrfs storage will support snapshots and a directroy storage not (except you use qcow2 files where the snapshot mechanism of qcow2 will be used). So I guess if you want to make use of those btrfs features, like the native snapshots, you should choose the btrfs storage.