If I remember correctly, the weapons bay was located in the upper secondary hull. When this movie comes out on blu-ray, I will be able to speak with more certainty.
It's not upper. The camera shows the launch tubes opening closer to the underside of the ship; you can tell it's the underside because the impulse engine is visible in the background, as is one warp engine for an instant. That means the weapons bay is somewhere slightly forward and below the shuttle bay, which makes sense if those tubes were originally meant to launch probes, drones, mines or ODST drop po-- er, I mean, "escape pods
" like the one Kirk took to Delta Vega.