Don't sweat the cruise missiles
You don't have to worry about cruise missiles if you stack a bomber with your battleships. As cruise missiles cannot attack bombers, they will self destruct if they cannot return to base after trying to attack a bomber+battleships+AEGIS cruiser (optional) stack. The only units that can attack such stacks are fighters which can do little damage to vet battleships or vet AEGIS cruisers.
This may require a carrier to act as a base for the bomber(s). The carrier can trail well behind the battleships so as not to be exposed to air attacks.
Alternately, form a stack of your battleships, carrier and any transports. Surround them with 8 stacks, each consisting of an AEGIS cruiser stacked with a bomber. These protect the convoy from all attacks except by fighters - and probably by nukes - if you are playing against the computer.
Such a convoy must include a carrier with at least 16 bombers. Eight of the 16 bombers are airborne each turn so that there is continuous protection.
From a few tests it appears that an opponent must sacrifice 15-20 fighters or more than 10 stealth fighters to break through the screening units. It is very unlikely that so many fighter aircraft can be concentrated at the right place and time. However, if you are expecting really tough opposition, stack an extra AEGIS cruisers with each bomber and include extra cruisers in the convoy stack. These can be used to replace any damaged ones so as not to slow down the convoy.
