There's no risk to the N900 - it just means that boosting the gain introduces even more distortion into the mix - to a level even beyond the serious amounts already present on the N900 (at least with PR1.3). We're not talking a bit more compared to other typical MP3 players, it's a LOT more. If you just want louder crud, then yes - whatever you're doing would be fine. I fully appreciate the drawbacks has little to do with your efforts though.

Someone (i.e. Nokia) needs to fix pulseaudio or whatever's responsible for this - I'm pretty definite it's not the hardware. It just makes it almost a complete non-starter for music listening if you have anything more than some crappy $10 buds.