And I again submit the possibility that the NACELLES is a retarded place to put the collectors in the first place since the ship's fuel is being stored in the primary hull, not in the nacelles, and it is better to place that collection hardware close to the bulk of the machinery that is going to process and utilize that incoming matter (namely, the fuel lab, warp core, impulse engines, whatever else) instead of having to pipe it all the way down from the nacelles just to process it, react it, and then send drive plasma back up TO the nacelles along parallel lines.
This gives is an explanation for a number of Trek oddities, most notably the lack of visible deflector dishes on some vessels (Reliant, Oberth, most alien designs). If the glowy things at the end of the nacelles are deflector elements instead of ramscoops, this simplifies 99% of all shuttlecraft/small craft/alien of the week designs that have nacelles and go to warp but don't have visible navigational deflectors: deflection might be an integral part of a basic warp field, with the ability to use deflectors effectively while NOT at warp is a trick mostly performed by advanced warships. The main deflector dish would then be an "extra" device, like the reinforced bow on an ice breaker, that can push interstellar particles out of the ship's way or scoop hydrogen clouds and interstellar particles INTO the ship to be processed as fuel.
The other thing is, the main deflector has a better field forward of the ship in the vast majority of Starfleet designs, so even if you must take the backstage sources at face value, the main deflector is still BETTER POSITONED to act as a ramscoop anyway. Even if one insists that past/current designs have not used it in this way, simple efficiency would probably result in FUTURE designs doing so, freeing up those spaces in the nacelles to be filled with other hardware like, say, Defiant style pulse phasers or even more deflector hardware.