Look at the LucasArts screenshots, the ones with the Star Destroyers blowing up. The domes on top of them are intact. Also, none of the crosshairs around on the ship are centered on the shield generator (but maybe the shots only shows the targettable weapons systems and not the other "destroyable" systems).
the developers were making the classic "those-domes-are-shield-generators-mistake"™, then most likely the domes would've been destroyed by the time the ship was heavily damaged. Hence, I hypothesize (spelling?) that the devs got it right!
Hears forummer thinking: "Thank you, but so the H[...] waht, you nit-picking SW n3rd?! "
Because most likely it means that you can't target the shield generators of capital ships, at least star destroyers, as the devs have realized that their shield generators are inside the ships. I made a game play discovery (maybe at least)! Maybe even one that's remotely important enough not to get me flamed for it! Yepee!