My personal opinion on the location of the M/AM reactors is somewhat complicated. I have two theories:
A) The reactors are in the nacelles, and the engine room we all saw in the series was actually a Warp Nacelle Monitor room, accessed by a turbolift (similar to the control room seen in the TNG Season 7 episode "Eye of the Beholder"). This is supported by the fact that the engine room on the original Enterprise shows a long glowing shaft leading towards the aft section of the ship, which would have been impossible to fit in either the saucer or the secondary hull (in the case of the latter, there needs to be sufficient room for the shuttle bay). Below are two images that show the engine room of the original ship compared to the nacelle control room aboard the Enterprise-D.
B) The reactors are either in the saucer or the secondary hull after all, and the long shaft in the engine room was actually smaller than originally thought. This room could even have been an impulse control room, with the reddish glowing shaft being the impulse engines, and the main engine room in the secondary hull (where the M/AM reactors are) never having have been shown. This is supported by the original interior set model, which shows the engine room depicted on the series as being located off the main corridor in the saucer section.