With the 3:15 rule, whether you're moving or not doesn't have any effect. It is how far the
target moves in that time that matters.
It might make plotting harder if you're using map contacts off though.
Another thing:
The game allows many things that aren't realistic. Stopping while submerged is one of those. Depth control of a submarine is next to impossible without some speed. I limit myself to 2 knots submerged. And nothing over 5-6 knots when using the periscope-too much vibration to make seeing anything possible.