I always go for the waterline myself, I'm not sure if it matters which ammo.
I'm not sure historically if submarines actually carried AP ammo or not. No merchant vessel, and no warship smaller than a light cruiser would carry any sort of armour protection. So no ship the sub would conceivably want to engage on the surface would require AP ammo. (not that a 3 or 4 inch AP round would have much armour penetrating ability anyway).
I suppose the AP round might penetrate further into the ship before exploding, and may be better for damaging engines/boilers and stuff like that.
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