Audacity is an awesomely useful tool for NWN and I use it not only for music but also sound effects, voice sets, ambiences, etc as well. (It's good for lots of non-NWN stuff too).
I presume I'm using a fairly old version of MP3toBMU, ie:- I've had it for YEARS. (I'd have to check the version number). I have NO idea how many bits of music I've used it on but since there's over a thousand entries in my ambientmusic2da, all the additions mine, it's evidently a lot. I've never had a single problem with it. Occasionally it tells me the bitrate of a piece of music isn't constant but you ignore that and it still works perfectly well in game. Never encountered anything you could call an actual bug or error that interferes with the program's operation.
Maybe, if there actually are bugs in it, they appeared in a later version than mine? I'll have to go and check its version number, just out of interest.
EDIT:- Mine's ye olde v0.35. Never had a problem.