One of the interception methods of sea skimming missiles is to dive from high above at an angle. There was an old video but I can't remember whether it was HQ16 or HQ9.
Therefor the interceptor need not fly at low level above the wave. This is like an eagle diving down from greater height on its prey on the ground.
Sea skimming missile was designed to avoid radar detections, once detected they can still be destroyed though at larger degree of difficulty due to short time between detection, tracking and impact on the target ship.