As previously stated, the biggest reason for break-in is for the spider. Spiders are made of cloth that is pressed and then dipped in epoxy. When you break-in a driver you introduce micro-cracks throughout the epoxy, which will make the spider softer. You can typically see a 20% drop in Fs over a lengthy break-in. But because Cms changes, your Fs will drop and so will Qt and Qe and Vas will increase.
Paul Roth of Credence did a test where he broke-in a driver for a long period of time and immediately tested the T/S's, let it cool down to room temperature and then tested the T/S's again on a M-130 model loudspeaker. *Note that this speaker has a much softer compliance than most car audio subwoofers
Here are the parameters immediately after a very long and hard break-in:
Fs: 46.9
Re: 5.5
Qms: 1.86
Qes: 0.33
Qts: 0.28
Cms: 1.64
Mms: 6.99
BL: 5.84
Vas: 20.69
SPL: 90.12
Le: 0.32
And here are the T/S parameters after it cooled back down to room temperature after several hours:
Fs: 49.9
Re: 5.5
Qms: 2.01
Qes: 0.35
Qts: 0.299
Cms: 1.58
Mms: 6.41
BL: 5.60
Vas: 19.99
SPL: 90.50
Le: 0.32
The driver he used had these parameters fresh out of the box:
Fs: 50.47
Vas: 18.64
Qt: .314
The greatest amount of change will occur right at the beginning of break-in, but the parameters will stabilize and show almost no change at all from continued use.
So what does all of this mean? For the end user, simply use your subwoofer normally. After a week or two everything should settle into a constant and you shouldn't see any change in the performance of the driver after that.