A third aspect comes in mind anyway: speed help overcome enemy's defenses, but is of little use to increase the amount of damage inflicted.
Quick back on the envelope calculation doesn't support your assessment.
Say missiles speeds are : 333 m/s , 1000 m/s , 2000 m/s.
Missile warhead to full mass ratio is 1 : 4 , explosive TNT.
subsonic :95% of damage done by warhead, the kinetic energy maybe enough to penetrate the hull.
supersonic : 66% of damage coming from explosive, 34% kinetic. The missiles are so long if the explosive is in the tail then it can detonate practically in the middle of the carrier , or on the opposite side of the destroyer : )
Hypersonic: 33% coming from explosive,e 66% from kinetic.
Means in the case of zircon the only reason is to have explosive is to spread the parts and make a conical hole in the ship hull. Actually, the decrease in the power of missile is marginal even with the removal of the warhead.
Just for record: 1000kg , 2km/sec means 2 gigajoule , and that is enough to evaporate 1000 kg of steel. it is 1.6m of steel armour equivalent.
So, the onyx missile at impact can evaporate 500 kg of steel, it is enough to penetrate 0.4 meter of armour .
The harpoon can penetrate 15-20mm of armour.