The same name / different inodes problem isn't a filesystem issue, it's a tools issue. Specifically, the fact that tools which modify files (editors, shells, archival utilities, scripting languages, any random executable) only see the local filehandle, not the fact that it's "supposed" to be a single chained copy across multiple directories.

There might be some way to muck around with that using attributes (at least in theory, I don't know of any that do this now), but presently, the only way to accomplish this is through workflow and integrity-checking systems (e.g., that "filename" at any of numerous specified points should be identical to and/or a hardlink of a specified canonical source).

Oh, and one more: since hardlinks apply only to a single filesystem, any cross-filesystem references are impossible.

I think you also end up with issues in almost all cases of networked filesystems: NFS, SSHFS, etc.