The best way to do it that I've found is to arrange a folder hierarchy of "where" rather than "what." So there's no one place with all the game's rock models, but rather firelands/towerofeternalflame/courtyard/rock01.3ds and so forth. "Where" doesn't have to mean a literal location; it could be playerbases/horde/rock.3ds or something. Though for most games, everything not tied to the player really can just be its literal location. It's crucial that these directories have a mix of models, textures, and whatever else you need, instead of a mass of parallel structures.

If there are automated tools, they should run on the entire asset directory and dump to a new directory in whatever hierarchy makes sense to the tool. When that turns out to be slow, check "file modified" timestamps in the tool instead of dumping required knowledge on the artist.

Getting artists to actually use source code control instead of having personal folders full of things like rock01_retouched_new_final_final.3ds is a bit of a pipedream, but you can at least put the asset directory under source control and make that the only way to see things in the engine.