Yes but how much effort it takes varies.
The main DS sound format is one known as SDAT. Few games use other formats but let us not go there now. I can't remember offhand what MM zero collection used but I will go with SDAT for now.
SDAT is broken down into three main formats
SSEQ, a midi like format. The instruments/soundfonts are a thing called sbnk.
STRM. Long PCM or ADPCM audio tracks (there is hardware support for ADPCM) that can be full songs if you want.
SWAR/SWAV. Small audio samples of PCM or ADPCM. Used for sound effects and more.
The compiler will strip out unused aspects of the code -- if the game does not use STRM then crowbarring it in there will not get you far as the game will likely not be able to call it.
However for New Super Mario Brothers a guy named Dirbaio hacked in a wave support for the game and released the code, you would in turn have to adapt ithttps://github.com/Dirbaio/NSMBCR/blob/master/source/wavplayer.cpp
If you are playing the cowboy then we have seen people break a song into sample length.. samples and make the SSEQ play back each sample in turn to do something like wave type playback.
I don't know offhand what sort of frequency limit your sounds are likely to top out at (looking at what I have ripped and the sound channel debug window of desmume most games seem to favour 11KHz, 22KHz, or something in between for the higher end stuff, however homebrew can go higher).
Depending upon what you find at fault with the music it could also be a case of lazy devs (Capcom are not known for high class dev work, especially not on the GBA and DS).. Go through the banks properly, sample instruments again and make it either truer to older versions or embrace elements from it.
If it is one of the other formats then they tend to be either wave/pcm/something that feeds directly into the hardware, something high level, something maybe known in games and very rarely are they truly custom other sequenced formats, though there are some.