Obsidian.md is doing them pretty well in plaintext. It has scaling issues, but think they come in a couple orders of magnitude above the "toy" threshold you mention. It might suffer a bit for a well-populated Zettelkasten until they optimize more, but for most users it'd be fine. I think a lot of the scaling issue was in the link graph analysis, and they've been steadily working on that.

To your point, I'm sure it caches a fair amount of that analysis in its .obsidian directory, but to mine, it can still calculate them from scratch on a new (or newly synced) note set. It does so invisibly the first time it sees the Vault (or the new file in the Vault directory, if you add it from elsewhere), so it's still portable, just with an indexing phase if you want to show a backlink or graph pane.

The important thing for me is that most other plaintext notes editors support the forward [[links]] that are the only real "source" data. The implied backlink analysis is just that, results of an analysis. It'd be nice for the cache to be portable, but not necessary.

Transclusion is where I'd agree with you, since that actually appears in the notes themselves rather than as part of an active sidebar. You're more or less stuck with proprietary software that knows how to look for anchors and render their targets inline, at least until/unless we get a generic format for it. But so far that's been more a reason I can't have transclusion yet than a reason why I'd move off plaintext notes in a directory.