Its health meter is always as full as that of the Snivelak Car.
Ratchet can destroy it by getting in and facing a wall and then firing the guns.
If you try to shoot at the Snivelak car with the lasers and destroy it, it would not be destroyed. Instead, in theory the bubble sub is destroyed without disappearing and Ratchet is inside it. Functions of Ratchet, like jumping, happen at the same time with the vehicle ones, unless he crouches.