^^ I'm betting they're smart enough to shield the entire system.
One would imagine EM shielding is in place anyhow - the carriers have a full NBC suite do they not?
Ehhh -- the only real "defense" is setting Circle-William (closing all outside ventilation and then activating the exterior water washdown system (think of hundreds of sprinklers) to soak the ship before, during, and after it enters a contamination cloud.