For example, you can use MPQ Explorer to look inside the package files of World of Warcraft, and see how they organise their tens of thousands of assets.
Generally, as others have said, it's by "where" rather than "what", or sometimes "what"/"where".
Beyond that - Perforce is the usual asset control system for these things. It offers the ability to tag files, which makes searching easier. When you're dealing with a huge pile of art, searching is basically the only way to go, so good tagging is very important.
(Source: I'm not a game designer, but I've worked with the complete art libraries of multiple triple-A games over the last two decades creating Machinima films, either working directly with the studio or on a modding basis. I know far more about the internal file structure of WoW, for example, than is probably healthy.)
OP, my bad if you were specifically looking for repo hierarchies. That's not the side of things I'm usually involved in :)