Wooden instruments like violins, guitars, etc certainly change in tone as the wood ages and dries. As the wood ages the internal damping diminishes, which allows more strongly peaked resonances. The thing is, this is all irrelevant when considering speaker "break-in" as people generally discuss it. People will leave the speaker playing at a high volume for 500 hours, and then hear a difference in the sound. They're not talking about the quality of the wood changing substantially in what really amounts to ~20 days. That type of chance occurs with years and years of time, and I doubt it would change significantly in MDF.
I think the only way I could be led to believe in speaker break-in is if someone did some objective analysis of speaker excursion in a controlled environment and showed that after extended play the surround element "softened" significantly enough to create an audible difference.
That said, I haven't heard any difference in my system over the time I've had it.
