I have a hacked N3DS set to run at full speed with L2 cache enabled. I've never experienced "lag" in the international version, although I have (a few times) run into a similar bug that softlocks the game with a monster onscreen at the end of a battle.
I think I have seen the battle lag, as described here, in the Japanese version though, while I was working on translating it (before it was announced for a worldwide release). But I never re-encoded the text or anything, the only changes I made were to plaintext files (.txt, encoded with shift-JIS if I recall correctly). This was on my OG 3DS as I didn't get the n3DS until later.