deduplicating is fine, the question is what it will do on a restore.

As far as I can tell from searching the web, duplicacy will restore two (or more) hard linked files as separate files. (Apart from the obvious one of losing the connection, your restore directory takes more space than the original).

Restic (again searching, but this I can probably test since I use restic) will restore them properly – i.e., preserving the hard link