I tend to believe people naturally think in graphical structures, not trees. It's sort of an impedance mismatch though because our physical world is tree based - you can't put an object in more than one container. So we're continually struggling to transition back and forth, to the point that we unnaturally try to force our thoughts into tree structures like outliners.
Exactly this. Also most information of any complexity has multiple “categories” it could fall into.
What you actually want is a network graph of concepts and notes. This will let you see relationships.
Trilium Notes[0] allows that. In fact I'm surprised that it's not mentioned here, because when I discovered it (via HN IIRC), it seemed to me that Trilium had already implemented everything I could have ever thought of for a note taking/personal knowledge management tool, and more.