Assuming you even *see* the hypersonic missile ahead of time, sure. Problem is, such drones do not have much loiter time so you can’t always have them up or they’d interfere with air operations... Were I to execute such an attack, I’d have the first wave of hypersonic missiles down at seaskimming altitudes before they get over the radar horizon of my targets.
Also, in the case of a ballistic hypersonic missile, they can avoid that by putting an armored nose on it. Even if you manage to destroy the thing as a functional missile, you’re still getting hit by several tons moving at a high mach number. Once the velocity gets high enough, you don’t really even need explosives if you have enough mass...
As the Sheffield found, even a subsonic missile that does not detonate can ruin your boat.