There is a way to get them onto ships. In Creation, look for two threads, one's called something like "Loadable Missiles", the other's called "Cruise Missile Tweaks". They explain how it's done.
Also, Korn469 has made a mod converting cruise missiles into dive-bombers (kamikazes??), and actually used some flags to get the AI to use them too. I would recommend that mod. (No offence to the other mods )
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I'm building a wagon! On some other part of the internets, obviously (but not that other site).