1. Aircraft carriers, helicopter carriers, and fleet commands are all examples of command ships. The command ship itself doesn't do anything (it's similar to a garrison or Long Range Division). It's the weapons that you put IN the command ships that do the attacking. The command ships just hold the weapons. As such, having 100 command ships would be unwieldly and probably useless. For each command ship you own, you can activate up to 20,000 naval weapons (similar to the military base/weapon rules). Fleets are separated based on command ships.
If a command ship is destroyed and there is a nearby command ship that can hold the weapons, your weapons will auto transfer to that command ship. If there isn't a nearby command ship, the weapons will be lost. Your last command ship of each type cannot be destroyed, only 99% damaged. As such, many people just buy 1 of each command ship. With just these 3 command ships, you can have as many as 60k weapons activated for your navy, which is enough for most people.
2. Using the War -> Navy -> Organize Fleets screen, it will list all your command ships. Select any two command ships, and you can organize the weapons between them as you wish, within the following two restrictions:
Only aircraft carriers can hold navy fighter planes.
Only helicopter carriers can hold navy helicopters.
There may be more, but these are the only two I've ever noticed.
3. As you know, Land Based Cruise batteries are based in your offensive military bases and are fired from there. If your offensive military bases are destroyed (or, if it's your last one, 99% damaged), you can no longer fire any land based cruise batteries. Relatedly, Cruise Missile Ships are the naval equivalent of Land Based Cruise batteries. They fire from command ships instead of offensive military bases. If the command ship is destroyed, you can no longer fire your Cruise Missile Ships. By and large, Ship Based Cruise Missiles are slightly more powerful than Land Based Cruise Missiles. Consult the weapons documentation for more detailed info.
4. Guided missiles are the ammunition for Guided Missile Frigates, another type of ship. They're smaller, less powerful versions of Cruise Missile Ships. Cruise Missiles Ship Based are the ammunition for Cruise Missile Ships.
5. Conventional missiles (and many other missiles) are constructed with (among other components) solid missile fuel. Once the item is constructed and you've purchased it, you no longer need to concern yourself with it. Conventional missiles are fired by Conventional Missile Batteries, which are more powerful, MUCH longer ranged versions of Land Based Cruise batteries, and are also based in Offensive Military Bases. Many people feel that the added expense for their ammunition is not worth the added range and damage they can do. You can consult the documentation to make your own determination. However, given you can buy 15 ship based cruise missiles for the price of 1 conventional missile, I've rarely used conventional missiles, except when you REALLY need to take that far away country now.
6. Navy Missiles and Navy Missile Interceptors are both defensive naval weapons. Navy Missile Interceptors (like their land-based Missile Interceptors) protect your fleet from incoming missile fire. Navy Missiles (similar to the land-based Defensive Missiles) are used automatically in retaliatory attacks against the attacking units.
7. Yes, and you'll find it invaluable. From the Simcountry Portal, click on Documentation at the top (in the same row as 'Live Chat', 'My Blog', 'My Site', and 'Forum'). Then, select '7. More Game Features - Weapons'. It will tell you anything you want to know about every weapon.