I do not understand how people have enough things to put down for posterity where they need linking between different documents, rather than a simple hierarchy. I suppose we are very different humans.
And your perspective today might differ tomorrow or in a year or 20 years. Think about Wikipedia (and other wikis) - there is no hierarchy. You can start at any point and, in a sense, there's a hierarchy of pages with the starting point at the top.
The Dewey decimal system has less ambiguity in both, and an alphabetical system would be unambiguous for archiving (if not retrieval).
I prefer to organize my notes functionally (eg internal emails, blog posts, links to read, reading notes) and then rely on search for retrieval. It’s not perfect but it lowers the friction, which I think is very important.
True, but .......
Full-text search solves many problems. And hyperlinks enable knowledge to be in multiple places at once and even remain normalized (i.e., it can be in other locations by reference). If your kb has an efficient 'include' functionality, it's even easier.
Most importantly, if you are using your kb well (by my definition [0]), you record high-quality knowledge that you've already engaged deeply with. If you can't solve the content ambiguity issue easily, it's just a sign that you haven't engaged and don't know it well enough.
Like if you want to brush up python for interviews, you're gonna want to take notes about specific things like heaps and string builders. You don't want to dilute that info with stuff you know will never be asked in an interview like how to build a TUI.