Yes, wave action could shift the line in the periscope sideways, disturbing the measurement. Also make sure you are not still in a slow turn.
What I meant is that if you move forward and say look to a ship on bearing 30. Then you are dragging your periscope line sideways (across the line of sight) with halve of your own speed (sine of 30 degrees= 0.5). If it happens to be at 90 degrees then your full speed will drag the line sideways, even if it is under a knot. This shortens or delays the time measurement. (depending if you are moving with or against its course) My advice is to be submerged and slowed down completely. OR turn the bow of the uboat right in front of the target, (or 180 just in front for an aft measurement) if you must keep moving for whatever reason. Then your speed is along the line of sight and will not have any affect on shortening or delaying the passage.
There are mathematical ways to correct for your own speed across a certain bearing but this requires a good estimate of the AOB, basically a more complicated formula. Turning is easier.
The above applies to WP equally as other sims though. So I don't see how this could be any different if you perform the procedure to the letter.
Way back there was the OLC GUI mod with early implementations of the RAOBF that used halved mast heights in the recognition manual (because it worked better using the periscope scale). But that couldn't make your speed halve of what it should be.
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