In a shooting war, you wouldn’t want a large conventional rocket attack or zodiac-delivered explosion, to disable the controls for scuttling the ship, and disrupt the chain of command for orders to scuttle due enemy action killing key crew members. The fog of war could lead to enough confusion and damage, such that a seaworthy ship is left afloat with no leadership, in dangerous waters.<p>Military ships can be difficult to sink, and willfully sinking them might not always be an option. So if the ship is captured, and held long enough to put warheads in the hands of a dangerous people, the weapons could disappear and appear in the hands of someone looking to extract a ransom to return them unused.<p>With submarines, this is not the case, even if the bottom of the ocean isn’t always unreachable. At least the bottom of the ocean sufficiently complicates salvage, past a certain depth.