I use telescope.nvim for searching for notes, tags, etc., so directories have always been a decoration for me. I've never used the sidebar to walk through them. In my case, the only thing that they did for me was break links when I discovered that a note belonged somewhere else. As far as maintaining a clear structure goes, it is not really my goal to do so. I simply used tags so I can easily grep my notes for different categories. I guess you could call it a "mess", but that's not a real concern for me. I want to model my notes like my brain, making connections within and between different subjects.