"Even aiming with periscope is hard and i am loosing (LOSING) the sight of my target, so firing torpedoes is simply a waste"
In real life if the waves were high, SOP was to decrease periscope depth to compensate. Standard periscope depth 66 feet was used when the target was close, at 15,000+ yards they would routinely go to 60 feet or less - 10 feet of periscope sticking up would not be a problem since it wouldn't be visible at long range. Same applies to heavy seas, especially with a lot of whitecaps, manually selecting 40-45 feet works just fine, even inside of 2000 yards. Rule of thumb, if the waves break over the periscope and you can't see anything but water more than 50% of the time, bring her up a couple feet.
As for attacking unidentified targets, subs on both sides were usually given a patrol area in which ALL targets were assumed to be enemy - the Germans in particular issued warnings to all neutral countries about "exclusion zones" where any ship might be attacked without warning, enter at own risk.
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