You bring up a pretty good point. Whenever I have a personal document that could go into multiple categories (eg a travel insurance certificate can go into travel, insurance, or finance folder) I place it in all 3 at once with hard links. What's more is that if I intuitively first search for a document in place A but it's actually in place B I simply place a link in A for the next time.
Before I learned a bit about file systems I didn't even conceive of such a thing being possible; precisely because the folder metaphor had imprinted upon me the physical world constraint that things can only be in a single place at once.