Never played the Imperial side of space missions, but if it's similar to Republic with different models, the big targeting reticule is just indicating that the frigate needs to be destroyed (everything on it). As to how to destroy them, there should be 2 shield generators on the frigates that needs i think 3 or 4 missiles to destroy each of them. To find out which ones are the shield generators, shooting your main gun at it, it will glow blue. Then the rest you can just use your main gun (the turrets and engines) to destroy.
Yeah, I've got that much. Destroyed every component on the frigate, but it still obstinately escapes at the 12 second mark. I've made sure to get the generators (well practiced from Mugaar Ice Field and Aeten Defense) and the engines. I've been playing the space missions since game launch, and this is frustrating.
To all the people who are having trouble with just getting through the missions alive, learn the routes first; the missions aren't hard for the enemies so much as the obstacles.