Well, trawlers engage in commerce, hence they are fair game.
In WW1 the U-Boats waged a regular war on fishing trawlers in the north sea which caused the british to use Q-Ships.
In the Pacific, the US and british sank hundreds of trawlers, sampans, junks and whatever. Problematic was that except for japanese waters, most of the people killed were not japanese, but Indonesians, Filipinos, Malay or whatever. The US subs still had no restriction in sinking trawlers which MIGHT feed japanese troops, even if "friendly" natives were killed.
In the med, both sides shot up small sailing vessels, often also manned by greeks, arabs or whatever....
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