You are talking about under 4k ton frigates, so you clearly miss my point completely.
Actually, size does not matter for current hypersonic anti-ship missiles and Onyx variants can take out an aircraft carrier on kinetic energy alone. And the layers of defenses you cite can't stop them.
Having three 10k ton ships instead of one 30k ton ship makes prefect sense in the missile era.
Sorry, but I have to say your are two times wrong.
In general terms, because weapons become ever and ever effective, ships need to scale up their hard (weapons) and soft (electronics, decoys, chaffs) defenses just to keep the same chance of survival their predecessors enjoyed twenty years before.
Frigates are a perfect case study, generation after generation frigates since the end of II WW have become larger and larger not because they needed more firepower, but for the opposite reason: the increase of opponents' firepower, being it from air or from surface vessels, dictated even more complex sensors, countermeasures and defensive weapons to maintain a fair chance of survival.
In specific terms, speaking of supersonic or hypersonic missiles, they are in no way game changers.
They could made several defensive weapons obsolete, but in no way they will made a ship obsolete.
Defense being a matter of sensors, electronics and finally weapons, large vessels are and always will be more susceptible to adopt new systems and weapons.
As modern airborne targeting sensors, clutter resistant look down/shoot down radar and light AShM made the fast attack boats obsolete, i.e. hopelessy unable to survive even the encounter with an isolated helicopter,, but neither frigates or destroyers let alone cruisers and aircraft carriers, new weapon systems will made obsolete those ships unable to integrate new/supplemental weapons and sensors.
Typically those ships too small, without enough room and power generation capacity, not those supposedly "too large".
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.
The real damage is generated by warhead dimensions and specific characteristics, and by the residual fuel.
Hitting the hull at 300 m/s or at 900 m/s doesn't mark a huge difference in the amount of damage inflicted: it's the fuze that will decide when to detonate the warhead, and it will be more or less always at the same deep inside the hull whatever the speed, because the aim will always be to detonate it within the hull before damages suffered from the penetration could severely damage the warhead itself. If the missile has to penetrate multiple walls, severe casing fractures and deformations could happen degrading the detonation effectiveness.
So, hull's dimensions will always be related to the amount and severity of damages received from a hit.
And no hypersonic missile, per se, could disable a carrier 300 meters long and displacing more than 100K tonnes, except the case of really lucky hits.
The hull is simply too large to get too extensive damage from a single hit.
It's the same as with a 500 kg bomb dropped upon an hamlet: it will destroy a building, cause more or less serious damage to nearby buildings, but it would do nothing, absolutely nothing, in turning the hamlet as a whole, "no longer functional" or unfit to be lived within and to conduct a normal life.