the hard linking of directories is a hack not really a feature. There's a good reason why filesystems ( including HFS+ when not being used for Time Machine) do not do it.
Another way, which is worse, is block-level deduplication. All of the above filesystems support it, as does NTFS.
I wish Apple would adopt HAMMER for Mac OS. It is BSD-licensed and more suitable for a memory-constrained environment than ZFS.