The fortresses they are in are technically airbases, and they are air units. They can only be used against ships that were stupid enough to go right next to the fortress.
Btw, you are NOT at war with anyone, no matter what your ambassador says. Sometimes it's not possible to 'technically' make peace with them in the civ engine, even though you've already agreed to it on the thread. You didn't attack any Prussian or British units did you?