While the only rule was that there had to be two nacelles, Matt Jeffries who designed the model said specifically that he wanted the design to have as little surface detail on it so that all the important things were on the inside and couldn't be easily damaged.
Technically not every species in Star Trek followed this rule: The Klingon's did not (The D-7 had two grilles inboard, two grilles outboard)
; The Romulans did*; All the other alien species it would seem that appeared in TOS appeared as a distant point of light, a spinning cube, a seed-shaped thingie, a bunch of lights (which was obviously reflective of a very poor budget for making good ship models)
and don't really count; Starfleet *DID* follow this rule, however.
Regarding Roddenberry's desire to sabotage FJ, you think he had the Refit Enterprise designed with outboard grilles simply to make FJ's designs look stupid?
* - It is not really clear whether the Romulans had warp-drive at this point in Star Trek: LCDR Scott said they only had basic impulse; On the other hand the ship did have nacelles and it does seem incredible how they would get this far out into space in that episode of Star Trek to be able to encounter the USS Enterprise without warp-drive. I have read that the model of the Romulan Bird-of-Prey was actually a very quickly-designed model which was partially based on the Constitution-Class saucer, and nacelles (Which is one of the reasons why it was written into the plot that the Klingons and Romulans were working together, and they just used the Klingon D-7's as Romulan ships)
-- the rapidly-created nature of the BoP could be used to argue that the nacelles do not really count and it is sublight capable, but as I said there really isn't any explanation other than warp-drive how the BoP could get that far out into space, and traverse as much distance to be able to encounter the Enterprise. Regardless it's nacelles have no grilles, not even inboard.