Various people have. It is pretty much the same as any other file system based hack -- you present the game with the model you want instead of the one it original had and as others have said it will require a machine capable of running hacked ROMs. You may or may not have to go one step further and sort names/call numbers at various points, depending upon the game. You can do this by injecting/overwriting the original or some kind of file system based hack/repointing if you are doing it within a game. the latter possibly being the better option.
The usual problems of mismatched animations, mismatched textures (and animations thereof), possibly overloaded graphics memory/processing and possibly different shader logic all still apply, perhaps more so by virtue of the 3ds having actual shaders and enough memory/it being far enough along in history for models to actually be reasonably variable unlike older consoles which probably did have the same skeleton/base setup, see it copied and then tweaked. From what I have read thus far the 3ds 3d graphics hardware is reasonably sane (smea first dubbed it something like older embedded open gl with newer stuff for shaders and the like bolted onto it), which is pretty nice compared to some of the older stuff like the insanity that was the N64 or in some cases the PS1.
