Is it safe to thin out Time Machine backups by deduplicating files?
No, you cannot run most deduplicator applications on a time-machine backup. 

Time machine makes extensive use of hard-links internally. Any application that is not aware of this will find hundreds or thousands of false duplicates (which are really hard-links to the same file), and proceed to hose your time machine backup. Apple also seems to do some filesystem-specific stuff in the backup too, which is why it needs to be on a HFS+ volume (either a entire drive, or a .sparseimage on a network share).

A lot of the complexity within the time machine mechanism is poorly or undocumented entirely, and if you break something, time machine will simply not work, without any meaningful documentation. If your deduplicator is hard-link aware, it may work, but it has equal chances of hosing something, from which you cannot recover. 

Really, there does not seem to be any decent tools for managing time-machine images, unfortunately.