You mean Zenith Bombardment ships, or something else? At least Zenith Bombardment ships are 400 energy. And mk 4 Zenith Bombardment seems to be better than either of the rebel ships.
The problem with high energy cost is the fact, that most of the game it's the only thing limiting fleet sizes. So, when it's a choice between 30 heavy bombers (mk 2 and up at least, I think) or a single rebel fighter/bomber, I'd just take the heavy bombers. Their range is not that big, and invidual ships die somewhat faster, they still seem a far better deal.
Of course there may be a situation in very late game when ship caps are the restricting factor and there's plenty of energy. Even then I'd consider mercenaries, or getting more turrets to free defending ships. I just feel that rebel colonies are at the moment only a penalty, getting a bad planet (hey, if it was good why don't I have it yet? Too far to reach? Too well defended? Then I may not get it anyway ) and penalties associated, or 100 AIP and possibly some ships.
Though, maybe it's just me, I just haven't reached a situation where those ships shine.