CIWS wasn't able to do much with them until block 1B in 2016 added FLIR to help target small surface craft. Even then, it's a challenge, they're harder to see/detect, they're harder to hit, they can be armoured, and you'd probably swarm them.

However, I'd imagine swarms of small missile boats are probably a bigger problem. It's a very cheap way to get a lot of anti-ship missiles in the air to saturate defenses.