Key for non Zettelkästen is to refactor notes and delete/store those older notes, this way you also throw away part of that nested hierarchy. You simply combine it with your own trajectory and ongoing inevitable specialization, software notes would house the notes about software that you actually use.

I'm not a big fan of Zettelkästen for this reason, there is no need for those if you go through note refactors and make it a yearly routine (I combine it with OS reinstalls and trying new programs). I don't care about note program longevity for this reason, I'm not bound to a particular program because refactoring also means rewriting many notes from scratch, based on older notes and current knowledge.

This refactoring/rewriting is also a good refresher and helpful for really internalizing broader concepts (which you then can apply to other seemingly similar areas).