Seems to me that surface skimming missiles would be easier to bring down than one coming straight down.
Shooting up geysers of water in the path of the missile could knock it down or off course.
I would think the ultimate hit would be a missile that penetrated the deck and continued right through to the hull, detonating and blowing a hole in the bottom. Oh, and coming in supersonic at least.
Am I wrong?
I suspect you are right but it might not make much difference.
Modern ships are not heavily armored.
If a missile comes in high then it is easy to detect early with radar and to plan the response. If a missile comes in at wavetop level, the seawater of any wave higher than the missile will block the radar. And if there are planned course changes near-in, there is less predictability when there are only momentary radar images.
IIRC, the AS-4 was designed to do a near vertical Mach 4 dive. Dunno how much maneuvering it could do during that dive, but you had only one chance at knocking it down, and the dealing with all the left over Mach 4 debris still coming at you.