While I abhore canon discussions and am not as great a nit-picker as thou art...
I am still at heart a Trek-Tech Head, and quite often get my dork on.
I like consistency in my shows, which Trek does often fail at...but look at how many movies/episodes they have to look back on and remember about. Ships are no exception, and while I'm quite overjoyed just to see when the visual FX guys actually remembered where they put the phasers last episode, I do like to see that stuff make sense in its own scifi fictional way. I do think there should be a reason for the nacelles to be placed on the secondary hull [unless there just isn't one] and there should be a practical reason behind putting such easilly damaged and wholly necessary things way out on thin little sticks for everyone to have an easier time shooting at.
I'm suddenly reminded [on the subject of nacelles] of an interview with Matt Jeffries who had questions about WHY Enterprise even needed an engine room when the "...engines were 75 feet outside the fuselage of the ship..." His words, not mine. But this does tell you that the model makers and artists really aren't in on the 'tech' side of things for most of the production.
But...if you want consistency...then you shouldn't watch Trek. They're not well known for it.
--guv