I think if you make it carry cruise missle, the warship will also carry nuke. Since a warship need to carry large amount of cruise missle to be effective, it will make the ship capable of carrying lots of nukes, making the game unbalanced.
Also, cruise missle cannot be fired directly from a warship, it need to be unloaded onto land, and then fired. These are limitation of civ4.
I think in civ4 cruise missle should be its own class, so we can make a warship carries cruise missle but not nuke. And also, cruise missle should be fired directly from warship. In real life, one warship does fire missle at another ship.