Oh, certainly that's what they were on screen. I meant that when the Enterprise-B was at the concept art stage the saucer extensions were originally intended to be shuttlebays before it was decided on them being impulse engines.
Either way, the impulse engines are the additions to the Enterprise-B that I dislike the most. I'm okay with the additional deflector dish housing, though I prefer the smooth uninterrupted curve of the original Excelsior's secondary hull and larger deflector. Less is more, as the saying goes.
I think certain FX team members may have taken them to be hangers, but John Eaves, who did the design changes, is on record saying they were impulse engines. Bill George lit them like impulse engines. That is one of many discrepancies between the model and the MSD we see on screen. Fortunately only the Impulse is seen on screen which makes that canon. And that location just makes no sense for hangers. When it comes down to it, if the person who designed the ship doesn't do the basic layout of the interior, then the drawings seen are screen are suspect.
The movie also isn't consistent in the deck numbering. Kirk was, according to dialog, on deck 15. There are no layouts where I can get that to be deck 15. It is more like deck 20, or Deck T in the TMP nomenclature. But if you take a look at the MSD, it is deck 27. Also, the main deflector is above the catalina wings instead of level with them, there is no lower hanger, quite a number of features are misplaced from where they are on the model, it has extra phasers, it has the Excelsior fins on the impulse deck that the model was lacking (Bill George took them off the original intending to reuse them, but John Eaves didn't want them on there so they didn't use them), the warp pylon mounting dome is off center (it is supposed to be centered), the supposed P/S hangers have elevators that go to a lower deck that would be outside the ship, the weapons that are on the model's secondary hull are missing, the dorsal phasers and RCS are in the wrong places. Generations would have been the ideal place for the model and graphic artists to get together so things lined up, but instead the graphic artists went with the flawed drawings they had. Not all that unusual as this type of error goes back to TOS and those flawed pressure hull drawings and the Phase II design using in TMP. So it is just kind of a normal thing, but it means the graphics are inaccurate and can't used for determining size. The only accurate drawings would be the Galaxy, Sovereign, and Intrepid classes as for those the model and the MSD were both done to design by the same designers. For the other designs, the model is at least consistent in most respects.