Folders serve to encapsulate several notes. Not a single note can be contained in two or more folders. This relation is unique within the graph visualization, one that is yet not being shown to the user. Something like this:
Love the idea, and have thought about it myself - I use a limited number of folders, but it would be very useful to see notes and groups like this. I have experimented linking every note in a folder to a note named the same as the folder to fake the same clustering effect.
Note (hah, see what I did there) that this doesn’t really scale for tags as they’re not unique to a note. Past three tags it becomes successively more and more difficult to create overlapping areas that make sense (not to mention allow for the effects of linking). See https://en.m.wikipedia.org/wiki/Venn_diagram