The problem with the Knowledge Graph ideology is that everything in your mind is already situated in a graph structure. That is precisely the problem. It’s big and complicated, with way too many connections everywhere. There’s no good in replicating that web in digital form.
Most "note-taking" or "knowledge management" software acts as a passive storage container. You create notes, shuffle them around into folders, add a few tags, and then they sit there. Waiting. Until you consciously remember to go looking for them.
Unfortunately, popular ≠ the best. The strict hierarchy made sense in the real world: a book can only be on a single shelf in a particular room. However, the restrictions of physical objects should not apply to abstract knowledge.