This is the most satisfying method I found.
This way the AEGIS, Nuclear Submarine and Regular Submarine can carry Cruise Missiles.
The Nuclear Submarine can carry Tactical Nukes, while the other ships can't.
No ship other than transport can carry Tanks/Infantry.
Transport can only carry Tanks/Infantry, but it can't carry NOR use (obviously) Cruise Missiles/Tactical Nukes.
The logic behind this is that in AEGIS/Submarine there is a built in system to launch Missiles, and only in a Nuclear Submarine this system handles Nuclear Weapons.
Obviously, a transport can not Launch a missile nor can it carry an entire silo.
You can always check the "Airlift" flag for the Cruise Missile.
Do not forget to check the proper AI Startegy flags (id est Naval Missile Transport) for the proper vessels.
I hope this helps.
Bye

This way the AEGIS, Nuclear Submarine and Regular Submarine can carry Cruise Missiles.
The Nuclear Submarine can carry Tactical Nukes, while the other ships can't.
No ship other than transport can carry Tanks/Infantry.
Transport can only carry Tanks/Infantry, but it can't carry NOR use (obviously) Cruise Missiles/Tactical Nukes.
The logic behind this is that in AEGIS/Submarine there is a built in system to launch Missiles, and only in a Nuclear Submarine this system handles Nuclear Weapons.
Obviously, a transport can not Launch a missile nor can it carry an entire silo.
You can always check the "Airlift" flag for the Cruise Missile.
Do not forget to check the proper AI Startegy flags (id est Naval Missile Transport) for the proper vessels.
I hope this helps.
Bye
