Well... want a semi-plausible real-science answer?
Bussard ramscoops, as invented by Dr. Bussard himself, are actually massive physical SCOOPS which, at reasonably high velocity, would funnel free hydrogen found in space into a collector. This hydrogen, as Bussard envisioned it, would then be used to fuel a fusion reactor based engine. Self-sustaining propulsion.
Now, in Star Trek, the bussard collectors don't have actual PHYSICAL scoops. Instead, they use powerful fields to attract free hydrogen. In fact, some descriptions say that they project a forcefield cone out in front of them.
The point is that the hardware that generates this cone is probably a very high-energy piece of hardware. At least as much so as the navigational deflector beam.
Now, the saucer is the main inhabited portion of the ship. The secondary hull has engineering, support systems, cargo, the shuttlebay, etc. Most of the crew, and their quarters, are in the saucer.
I'd say that the bussard collectors are on the nacelles for the same reason that the subspace field coils are in the nacelles... they generate energy that could be potentially hazardous with prolonged close-up exposure.
Alternatively, there's also the original concept... which was that the warp nacelles were self-contained... they had antimatter generation, matter collection, matter/antimatter reactors, and warp field generation hardware, all in a single system.
Take your pick. Either is equally valid, and neither is necessarily true, but those are the most common explanations for why this is the case.