the real fear would be large missiles/small ships with Naquahdriah-based hyperdrives, and naquahdriah in it's plating. it drops out of hyperspace, and then the hyperdrive goes critical and explodes, with gigatons of energy.
the real threat of this is not bypassing shields or anything. a carrier (or better said, a starbase with the abilities of a ship) would be able to sit 10 LY away from it's target and pound at it with Hyperspace missiles, jump to hyperspace, (and due to lag), the enemy will never know where it came from. extrapolate the Carrier's location via the Missiles, and you end up where it WAS. by then, the carrier has already relocated and the next barrage is under way. meanwhile, fighter/gunships are launched, along with a few Hyperpods (hyperdrive "torpedoes") which envelop the Fighters in a shared Hyperfield, and brings them to their target. the Fighters then launch conventional naquahdriah missiles, while ensuring any fighter cloud is rapidly taken care of by prematurely detonating a nuke. by the time the carrier has to enter battle (if at all), the enemy is severely weakened or destroyed.
which is why generational ships are needed to carry your population, and special cargotrains to mine from planets