The break in loosens up the parts. The consensus is that speakers sound better after being broken in. Some speakers can sound shrill and "stiff" and breaking them in can tame the ragged high end. This article explains it better than I can:
http://www.premierguitar.com/Magazin..._Speakers.aspx
Stereo speakers are a different animal. They have synthetic cones and surrounds, which do not loosen up over time like the paper cones in guitar speakers. Stereo speakers are typically played clean with no distortion in the signal, their purpose is to reproduce recorded sound. Guitar speakers generate music and there can be lots of harmonic distortion in the signal.