While the Civ2 AI was fond of CMs, it for some reason always targeted Battleships. If four Transports filled with Armor turned up on the horizon with a lone Battleship following, it'd waste whatever number of missiles necessary to sink the Battleship, and then happily watch the Armor rip thru its cities during the next turn. Ugh.
As I've written in other threads, I'm kind of a fan of CMs in Civ3. Ability to fire from ships'd be nice (my mod allows this), but the range shouldn't be increased much without increasing the cost, or they'll be too effective, in particular since the AI is really bad at exploiting modded units.