I'm not sure if the new conning towers would decrease dive-speed. I think the frontal surface of the U-boat would determine how hydro-dynamic the thing is (thus affecting the dive-speed, or submerged speed)
Does the conning tower actually gets bigger? I thought there was just an extra section for AA placed at the rear of it.
If so, I do not think it would decrease dive-speed (if that's programmed in GWX at all).
On the other way, extra AA means extra weight, which will get you down quicker
