All kidding aside this is an example of an asymmetrical threat. Just as small boats can be legitimate threats to major combatants, I can see how a missile-armed flying boat that can fly literally at 0' could present a major defensive challenge, especially in very confined waters.
Yes, they would lose a butt-ton of these things impaled on CIWS rounds, but a couple could get through and seriously damage or sink one of our largely unarmored surface combatants. Our pain threshold is notoriously low. Just like terrorists, they would only have to get it right once. We have to get it right every time.