not by default, it uses rsync internally which does support hardlinks, but you need to add the flag in the settings (custom rsync flags).
having said that, users have reported some issues with hardlinks, unraid shares (can't remember the details)
my suggestion, use another tool if you have hardlinks: i don't use them so i can't validate/test them, there have been report of issues (similar to yours) and finally, it's not a good idea to change the rsync default flags that unbalanced uses (i may remove the custom flag setting altogether)