All else being equal, fishing boats are for Germany better sunk than a float for Germany because it decreases Britains ability to feed herself and lowers moral.
It is to consider whether long term consequences would discourage an attack. For example, torpedos can be used later on bigger targets, but a few shells will probable not be missed. There is also the danger having ASW forces directed to you, and this varies according to proximaty to enemy land and stage of the war.
Any moral arguments against attacking fishing boats can be used against attacking any unarmed ships.
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