Not sure why people defend an archaic organization form here - reflex ?
You are perfectly right that files and folders are simplistic, and should naturally adapt to the pov that are more information rich/valuable. Hoomans tend to collapse a high-dimensional structures to 0D to 3D, so we can manage the information. In that sense, a std hierarchy is only ONE pov over a ton of pov over the same content. A standard hierarchy is only a low 2D dimension structure that are our first attempt at organizing information. It's not wrong - just imprecise af.
Anyway, hardlinks are a small step up, can build wild static structures (like a oneshot filesystem in Guix), but is cumbersome to control in multi-dimensional information structures. Likely not what you want, but look into fuse file systems if you want to move on to a dynamic file system hierarchy. An interesting one is a tag file system. It turns a standard limited hierarchy into a much more dynamic file-structure where a file can - and does - belong to a bunch of tags - file type, size, group, comments, whatnot. There are many many fuse fs that can convert anything into a better structured file system. Tagging is a step up from a dumb 2D hierarchy, but maybe a graph file system is the ultimate freeform dynamic filesystem that can present all the pov's we could possible need ?
Go for it.
You have to think in 'information dimensionality'. A yes/no toggle is 0D, a list is 1D, a list of lists (std hierarchy) are 2D, a list of list of list are 3D etc. All information storage types are one of these dimensions. Think of a graph-base file system with nodes and edges between everything. Now, imagine a filesystem where you flick a switch and the whole structure shows another pov ? Maybe you want the whole thing to be shown as file-type hiearchy, or only parts of it. Maybe you need to show movement in the structure, so everything are in a temporal/spatial hierarchy, maybe you are only interested in dependencies ? Relations ? Other 'weird' metrics ? ..and so on. The main problem is to manage, find and show the needed information in a higher-dimentional fs.
Technically a normal file is also a list, or another ordered structure, but in this sense, they are just a node with further dimensionality.
There's a TON of information layers locked away in our normal filesystem hierarchy, so OP are perfectly right, and people here have no imagination or even a world model of information structures..