The answer to sub orbital, High Altitude, and Sea Skimming Hypersonic missiles fired at Naval Warships is a dedicated ship mounting a Neutral Particle Beam Weapon.
On September 4, 2019, Defense One published “Pentagon Shelves Neutral Particle Beam Research” by Patrick Tucker that said, “In March, Defense and military officials announced their intention to test a neutral particle beam in space in 2023, and requested $34 million to develop it in the 2020 budget. Congressional Democrats weren’t pleased. In May, the House Appropriations Committee stripped the beam’s funding from their version of the defense authorization bill.”
Hypersonic missiles can easily be modified to make Microwave and Laser weapons useless against them. On the other hand, there are no practical defenses against a Particle Beam Weapon. They operate near the speed of light, and so any Hypersonic missile would be, comparatively speaking, “standing still.”