I just found out that I encrypted nds files with eNDryptS Advanced and then trim it with dslazy(file size become smaller). Then use NO$GBA version 2.3d to run the game and it can run a bit faster. I don't know there have bug or not but I think it sure can run a bit faster.
Sorry for my bad english.
Currently tested games: Final Fantasy 3 and Pokemon Diamond (JAP).