Not sure about torp speed in rough seas, but it certainly does play with the depth. It also does change the ship speeds, if you have that option turned on you can see their speeds vary by a knot. I like the heavy seas on damaged ships, sinks some you wouldn't have gotten and speeds up the others greatly. And it allows me to curse 'Verdamnt!' when I have my scope being blocked by the waves just like in Das Boot :rotfl:
A ship that might take hours in calm seas goes like a rock in the heavy stuff. And while those bow hits work wonders (GWX) even in calm, there's nothing like seeing one go down helped by a big wave that just sucks the bow down and never release it.
T.