No, I get the same thing (in SH3 too) and it's not wind or the motion of your submarine. Sometimes, when using the deck gun, the shell will appear offset in the sights. Usually it's to the left but I'm sure I've had it off to the right in SH3. The shell doesn't seem to 'drift' into that position but appears off centre from firing and stays there as it heads to the target.
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