True. This is a very different class of drone. What is the defense against an adversary who releases a thousand quadcopter style drones against a US aircraft carrier?
It's definitely a concern as part of a larger attack, but I don't think a quadcopter drone swarm alone is likely to sink a carrier or leave it combat ineffective in the long term.
A few nice miniguns with radars sensitive enough to pick up birds that fire flak.
Auto cannons.
Missiles.
... Lasers.