Well, the problem with using file names/URLs for unique identifiers is that they might change. So either you don't do that or you need some piece of software to update this. With a note title (and thus file name) of "[2020091149] Conversation about Note Taking on HN", I can just reference the part within brackets, and it also gives me the timestamp if the file metadata ever gets lost in sync.

But yeah, I don't have that many cross references now, this is one part where I'm looking for better solutions that don't depend on too much technology. Thus my Zettelkasten research. Probably will implement a lot of this with scripts and shortcuts (I'm quite fond of tools like Textexpander/atext for this).