For the most part yes you just swap the models over for 3d games and as long as the models use the same base setups (don't have the first point in the model be in the foot for say a town NPC and the tip of the head for the main player thus messing with animations).
Two broad scenarios, maybe three for why it is not doing what you want.
1) You did not get the right model. Maybe the devs left a prototype one in the ROM for whatever reason and you fiddled with that.
2) Some games do things by file order. If your unpack tool respected the file order it might have put it back together the original way, assuming it was not a simple forget to press save thing.
3) Some models are within sub archives, or multiple things within a base model (less so actual models as much as multiple textures). This then messes with the ndstool unpack, copy-paste-overwrite models, rebuild ROM approach.
Also if you are loading a savestate to skip back to test it then don't, or at least figure out how to force a redraw and/or regrab of things (for the most part that means going from the start or far enough back in the menus that start from scratch and finger on the turbo button while the dev splashscreens happen is easier. If it is corrupted music, 2d graphics or something then easy enough to enter a room/level/skip a track but 3d graphics is more annoying).