I believe that the majority of paddlers would shorten their paddles 1-2 cm in rough water because of the higher/choppier stroke rate, the frequent accelerations, and because a too-long paddle tends to clip/get caught on waves during the exit phase of the stroke.
Air strokes are a hazard in rough water and more likely with a shorter paddle, as you noted, but a longer paddle is the worse of the two evils.
Erik