You can try to add the exefs from the updates to the romfs so you load a fully updated Smash from HANS, but that's really hard. I tried myself, and I coudn't get anything to work. You could check comments on the thread about custom music on Smash.
http://gbatemp.net/threads/guide-smash-4-custom-music-with-hax-2-5.401079/
@Damon_girl About Tomodachi Life, I've not seen any thread about it. I don't have the game, so I can't try it myself, sorry about that. If it doesn't have any update, you're okay to do it. If it has updates, well, it could get the same issue as Smash when trying to load it through HANS. Sorry, cannot really help with it. Let's hope HANS gets new releases with this problem fixed.