Which kind? 'Hypersonic' is a speed regime, not a technology in itself.

Hypersonic cruise missiles are not in the purview of ballistic missile defense, unless they have a ballistic stage, in which case they might be. Hypersonic boost-glide vehicles, having a ballistic boost-stage, are countered by some forms of ballistic missile defense, but not all.

Ballistic missile defense is a defense against ballistic missiles. Not torpedoes, cruise missiles, artillery shells, nukes smuggled in shipping containers, frogmen going up a river with a SDV, or anything else. Pretty much just ballistic missiles, or at least weapons with a ballistic boost stage.