Taking out the enemy carrier by 'backing up to it' and using tomahawks was my favourite 'win' tactic from the original :-) Being able to launch a limited-range subnuclear warhead from island-to-island would be great, so long as you can be actively involved with it...
e.g. You have to successfully land a manta with a 'homing pod' on the enemy island
or You have to have a walrus laser-designate the spot for the missile
or A walrus dispatches a 'squad' of marines who can infiltrate and use the walrus' long range comms pod to relay targetting back to the island...
or The carrier has to be in range of the island.
The interesting thing is that if the cruise missiles have a limited range, then you can use them to crack particularly hard nuts by making an island into a temporary bridgehead, but you cannot then sit a silo back on your stockpile island and rain destruction anywhere (a-la nuclear weps in Command&Conquer games).