(The following post is a opinion, I dont know actual reasons, Im just saying what I think is more likely be true)
Music has to be loaded to RAM too, dont forget.
I can see the stage musics being more compressed/shorter than the ones that are Music Player only, to avoid consuming too much RAM during a match.
After all, 3DS has only 128MB RAM, rounding 100 (assuming OS consumes the remaining 28MB). A high quality music file can be up to 10MB, thats too much to load just for music in a match, but it would also be unfair to NOT put high quality music in the game at all because of this.
You should never use all (or close to all) avaliable RAM, to avoid "worst cases" slowdowns, and I believe Sakurai Team knows it very well, after all, even the 3DS version run in solid 60fps