You could read the chapter on deck gun usage from U-boat Commander's Handbook that was released in 1942. Deck gun usage is ok there and deck guns were used, but not if there was a risk of being attacked while doing it. There was a conflict between Prize regulations and what really was possibly for a u-boat to do near the English coast.
I don't think it ever was ok'd to use a deck gun in a situation where the merchant was armed or near the English coast as there was a big risk of getting attacked while using the deck gun. However I think that the deck gun was used all the time in the first years of the war in safe areas, like Central North Atlantic for example.
I wasn't clear enough on the German military doctrine either. The doctrine doesn't care if the order is specific or not. A specific order can be broken, if the commander makes the assessment that breaking it helps in achieving the objective better than what the order says. The commander takes the responsibility of breaking the order. If the decision turns out to be correct he will not be punished in any way, it might even help his career. If it turns out to be wrong, he could have no consequences, or be jailed or even shot.
What I'm saying is that I think it would be totally realistic to make a judgment of attacking an unarmed merchant in airplane free areas with a deck gun in any year and totally unrealistic to attack an armed merchant with a deck gun, or attacking a merchant in day time with a deck gun near the English coast with it's airbases.
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