All depends on what they are using
a torpedo or cruise missile could be conventional or nuclear while a ballistic missile would be assumed to be nuclear
cruise missiles are much easier to engage versus a ballistic missile but it does have the advantage of the fleet reacting to it as a conventional attack
remember a USN officer who once quipped that if someone fired an Exocet at a battleship they wouldnt be concerned as the armored sides could take that kind of hit easily
could see a very overconfident officer saying that as his last words as he finds out the hard way its a nuke
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