Volume snapshots are a better way. The only filesystems I know of that support them are ZFS, BtrFS, and HAMMER. I'm not sure if snapshots are implemented using hard links or if they are more fundamental.

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.