According to Lucas in an interview the domes were just sensor towers. However, in the Ep6 movie they seemed to suggest they were "shield generators" because an a-wing destroys one on the super star destroyer then the very next thing we see is an imperial officer shouting "They've destroyed the forward shields!" Everyone believed they were shield generators till Lucas said otherwise.
I actually think there's a lucasarts video game though where you have to destroy the two "shield generators" on the top of a star destroyer then a third one underneath before you can make a run at the Star Destroyer's bridge. It was one of those "pulled by the nose, just press to shoot" ones. I almost want to say either Rebel Assault or Rebel Assault 2.
And personally, Having them as shield generators gives us a much better option, gamewise. They make great targets that people naturally want to shoot at because they saw them explode in the movies. I'm not going to sacrifice that kind of "desire" easily 
Fear the Woodzilla
