Well, yes, but that is a different question. We can also discuss if always sailing under strong winds merits further penalization (v.gr. +10% each turn, or whatever).
What I meant is that firing without the lower battery because of the wind should have the same increase of "fatigue" than a ship firing with the full battery.
As Brendan said, our "fatigue" is an abstract concept which includes firing guns, handling the rigging, actual fatigue, etc. If a ship fights without the lower battery, the remaining gun crew would be employed in other tasks, maybe in the rigging due to the strong winds or maybe moving the guns up a slope, as Munrox said, or maybe... What is sure is that this guns crew should be not free. In my opinion, that can justify the same increase of "fatigue" in both cases.
Other question/suggestion that may arrise concern the split of the "fatigue" into two factors, that are, "fatigue due to firing the guns" and "fatigue due to handling the rigg", but that most likely will increase the algorithm complexity

. And still both will have large degree of abstraction.