Seemingly the contemporary advice for running a zettelkasten notes system involves hyperlinking (reasonable, sensible), but to do so with extended markdown through wikilinks. (See: Introduction to the Zettelkasten Method.) The go-to program to manage all of this is, it seems, Obsidian. There's nothing wrong with any of this, though I am hesitant to move away from CommonMark and I am (slightly) hesitant to rely on Obsidian for my organization. I also don't think it's necessary to use a different file browser from what's already on my computer: Obsidian really does little for me that Finder itself can't do.

On the opposite side, this seems like a perfect use for Finder's tag system, however, those tags are only useful within Finder and macOS, so there's another interoperability issue. Although this is a minor issue since tags should first exist inside any note.

I do like the idea of using a BibTeX file for any references, especially now understanding that it is a flat file database.

So, I think I will use a simple "Notes" folder in finder with MD files as just a single level to collect notes. I like the idea of a unique identifier, but I'd rather use something simple and more readable than a date/time string. I think the file should also have a very brief but descriptive name. An "Index" file can act as an index. Eventually, there'll need to be some organization, but I think new sub-folders can be made as necessary as the body of notes grows and demands them. There won't be hyperlinks between files, but they will continue the human-readable references so they can be easy to find. (Sub-folders could take a simpler identifier, too, I think.)