Sound on nitdroid was a bit louder , choppy and with more bass . Personally I thought n9 speaker is not that sensible and weak that a little higher volume would damage it this hard ... my fault .

So you mean it was 100% on NiTDroid or some artificial tweak was used to increase it? This issue would certainly do with more awareness

one of my N900 speakers blew up (the right one) due to loud sounds on nitdroid.
Nokia speakers aren't exactly the best in the world, nitdroid settings aren't the same as maemo5 or harmattan

It is caused by software, yes NITDroid could do that. When using NITDroid and playing music on it, I noticed the sound VERY high, higher than usual. The sound in NITDroid is what the N9's speaker can't handle. If you use tweak S in N9QTweak too, raise it to 100% and play music. Keep playing music for 10 minutes and you will get a smell from the speaker as if it is on fire. And the speaker will become warm or hot. If you keep the music playing for 2 hours I am pretty sure the speaker will be damaged. This fire smell effect also applies when using NITDroid (without any tweaks). So NITDroid's sound is as if MeeGo's sound on 100-110%. It could severely harm your speaker. So I am pretty sure NITDroid caused it.
Edit: Plus, Nokia never officially supported NITDroid so they won't enhance the quality to fit your Android device.

I'm sure the device will be repaired within warranty if u just flash everything back and tell them it just happened listening to music (well, u don't lie.. just dont tell them the nitdroid part)