One day one of them will sink a carrier.
Possible. Subs have sunk fleet carriers before (the HMS Ark Royal, the IJN Taiho, the IJN Shokaku, the USS Wasp...) However, Having our own SKK's with AIP technology will not help until they have longer range and are faster. Until then, nuclear subs will have a clear advantage, especially for the US navy.
Our new Virginia class SSN's were designed with littoral combat in mind.
The Littoral Combat Ship will have a few modules, including one for anti-sub warfare.
I don't see one of the new subs catching a carrier group off guard soon.