In Empire at War, missiles were individualy spawned projectiles; their own entity if you will. This allowed them to be targeted by weapons and whatnot.
I came to Sins from modding EAW. Honestly, the modding aspect of EAW worked a lot better. For example, in Sins, I can't allow a planet to build a starbase because it's not a "PlanetModule" entity. I also can't give shields to fighters because there is no shield variable defined in the "Fighter" entity type. In EAW, if you wanted something to have a shield, add a line in the XML file. That's all there was to it. If you wanted a planet to be able to build something, all you had to do was add it to the menu. It would build no matter what "type" of thing it was.
I find this very frustrating as it severely limits my options and hinders what I'm trying to do. I don't want to have to have a frigate build a starbase.
I want targetable missiles/bombs too.