Network is better than linear
Networked notes are more powerful than linear notes, because they allow thoughts to be connected in different ways. You can create hubs of different subjects and link the same note to different subjects.
A linear system of notes has two links- to the previous note and to the next one. A web has multiple notes at different points.
- I wrote a blogpost about this here.
In providing a system for manipulating this sort of information, the hope would be to allow a pool of information to develop which could grow and evolve with the organisation and the projects it describes. For this to be possible, the method of storage must not place its own restraints on the information. This is why a "web" of notes with links (like references) between them is far more useful than a fixed hierarchical system.