None of the rsync changelogs call out the ability to recognize hardlinked directories. (My source is a Time Machine backup drive.)
Now, maybe it deals with that unusual feature correctly. Maybe the hardlink detection is generic enough that it just works.
Some days, you just have to ask yourself, <Am I the sort of degenerate who's going to go read the rsync code and see if it properly handles hardlinked directories?>
(The answer is yes. It's not obviously broken at first glance, but I'm not going to go further than that.)