I do subfolders based on type of VAR content, like looks, plugins, etc. This is purely a file manager option to manage my VARs, which I do manually, keep only the latest versions and extensively remove and alter the VARs.
Duplicate VARs are ignored by VAM but they're a waste of space and show up in the Error Log. Should you take up subfolder use, duplicated VARs won't break anything and their overall impact is negligible, but you should still try to avoid them.
There's a bonus to doing this that wasn't mentioned, is that if you move VARs to specific places you get a good idea of what VARs you have, from what creator and what the're for. That knowledge is useful too.