If you make one that has a hangar with a CP for players to spawn in what happens if the ship is destroyed? Will the CP be removed when that happens, or is that not possible to do?

The CP and any other objects not directly connected to the main frigate model will remain as they are, unless you script it so that all objects associated with the frigate will be destroyed once the main frigate model is destroyed. This is similar to how the auto turrets are also destroyed when the stock frigates are destroyed.

Ah, but after thinking about it the model I've made is too small to use the stock hangar and I don't think underside hangars would work for AI, I might just release 2 versions and do a hangar one in the future.