I worked on another sync client's representation of filesystem structure, and came to the same conclusion. Hard links enable some cool behavior, but in retrospect added more complexity than anyone expected. Migrating to shortcuts / soft links seems very reasonable - I wish I had started there.
Every file is essentially the master pointing at the same inode. So the file remains as long as any of the hard links exist. With soft links if you delete the master file all the soft links stop working.
Apple's Time Machine uses hard-linked directories to replicate your home directory again and again, but with only the changed directories/files actually taking up space. The unchanged directories are just hard-linked to the previous versions, so any one version looks like your entire drive, but it takes much less space than full copies.
