It isn’t just the footprint that needs to be considered. The motors used on some missiles produce “stuff” that is not good if sucked into a jet. Thus before firing such a missile you have to either stop all aircraft engines still on deck, or risk trashing them.

The launch trajectory has also to be carefully considered vs launch and recovery paths of aiircraft.

So personally I feel that missile systems on board carriers should be minimised to at most self-defence. And even then it is not always appropriate