You don't have to have the submarine involved in any ship missions.
Exactly.
As for the naval bombardment thing, I ment would it be possible to combine a large, moving ship with CoC's arty.
Imagine: A mission where you play the commander of a ship, you have to avoid enemy ship trying to sink you while providing arty support for ground troops.
In a big naval fight, CoC's arty would be great, having to calculate distances, using scout hellicopters and planes to find enemy ships, then bombarding them from a distance with your big guns (Or cruise missiles). The key is hwaving it mobile. If it's just a stationary object, then it's just decoritive.