The soft suspension parts of speakers and sub can lose some tension over time, and this can lower the resonant frequency. It would never be audible unless you A/B'd the same model speaker, one broken in and one brand new, and even then the difference would be slight at most. I don't like saying that because people who think break-in can make a serious difference might use it to legitimize their beliefs. What audiophiles normally mean by 'break-in' is a myth.