I had a similar problem with obsidian, i kept having to refactor the folder structure and it let me do way too much nonsense imo that stopped me from just writing content/taking notes. In comet there is a tag view scoped to each notebook so you can break a notebook up by tag (without the notebook being polluted by all tags), and even further the more tags you add. You can add a tag by just putting a hashtag in the note content.