What's probably happening is that the menu is loading a placeholder logo that was never meant to be seen since the game was never intended to run on a non-Japanese system. I think the only way around this involves modifying the game itself.
So I just got Japanese Tomodachi Life on my 2DS (NA region) but something weird occurred. So, on Luma, I have game patching enabled and there are absolutely no issues running out-of-region games, but for some reason after the game had downloaded...