Absolutely. In fact:
(1) Magnepan -- says right in the owners manual that the speakers pick up additional bass extension after running some 100 hours (without rechecking the manual on my Magnepan 3.6s I think that was the amount of time). I can also say, after owning 4 pairs of Magnepans over the years, that the speakers improve in other ways too after burn-in.
(2) Beyerdynamic -- I was recently speaking with a B. representative who related that their phones develop additional bass and smoother highs after burn in. That's been my experience too with the Beyers that I have, and other phones too.
(3) Other manufacturers - It's a fact that there are numerous manufacturers (of both speakers and other electronics) who state in the manual that item's performance improves after a period of break-in.
Conclusion: Break-in is real.