The sound being choppy is the direct result of two things: the emulation speed still not being at 100% and No$ incorrectly handling multiple sound layers.
Case in fact, those games with little to no 3D rendering (TWEWY, Picross DS, Mario and Luigi: PIT; just to name a few) have no such problems, unless there is a cluttering in sound effects in cutscenes.
Sadly, we haven't had word from Martin in what amounts to a year now, and we can offer no information on whether and when the new version of No$ will come out and what updates it will include; without resorting to senseless guessing.
EDIT: Only thing you might try is the noise remover utility in the External Programs thread (Tool.7z archive, "A" subdirectory).