Now, seeing the original, I... still don't know the right way to operate a system like this. Instead I took the core concept of keeping notes as atomic as possible and use that with linking as many notes as possible together to form new ideas. And that's it. I don't worry with weird file names or the "correct" way that things should be linked together. Obsidian.md has been a great help with that, but any Wiki software will do the trick.
I'm glad I'm free of the old mentality I had. I spent 95% of my time trying to figure out the perfect system and how to operate it rather than writing. Now I just write.
In my case, I just use one Org file per card. I don't use internal links. I prefer search (ripgrep) and index files, where I list sequences and entry points to topics. This also allows restructuring my Zettelkasten more easily once new ideas emerge, or once I realize my old ideas were wrong.
In other words, I am trying to go one step further by decoupling cards (ideas) from links (relationships).
I do use external links, and in particular DOI links to publications. But I keep these in footnotes. Hence, my zettels look really spartan. It's just plain text plus footnotes.
Aside from Org and Markdown, TiddlyWiki is pretty neat. It's pretty good for transclusion. That can also be achieved in single-file Org Zettelkastens / wikis.
Roam Research handles this well with the block lists and block links (linking a block shows the content of the block rather than a link.)
Alternatively, I have found that a combination of OS links (symlinks or hardlinks as you prefer) with markdown files works fine. You can then use a static site creator to create different HTML views. As another view layer, you can manage these files with a file manager. Even better if the file manager can show text previews as large thumbnails. With the file manager, you can also manage the linking and other file operations. Then you can use any editor to edit the files. This is relatively complex, but more flexible while still using flat files.
I have tried to like Obsidian, but it ends up just getting in my way like any other Electron note app which attempts to re-create something that the base OS tooling can handle by itself.
I do like Roam and I have been trialing it along-side my above described flow. My ideal is using Roam for atomic notes and my own system for long form and anything else which isn't "atomic notes." I also won't put anything sensitive in Roam. I have been trialing it for months now but it's still sticking.
I think people who have problems with the idea of the Zettelkasten overthink the parts which they don't really need to think about at all. You don't need to recreate the stuff which the digital system handles for you in the background.
How to Take Smart Notes: One Simple Technique to Boost Writing, Learning and Thinking – for Students, Academics and Nonfiction Book Writers