The engineering section of the Enterprise has always been referred to as the "secondary" hull. That is why they call the saucer section the "primary" hull. For the writers to refer to the secondary hull as a nacelle is silly.
No, it's not. It's only silly if you cling to the "secondary hull" thing. I'm perfectly comfortable with the explanation that "aft nacelle" is the secondary hull. I know it doesn't mesh with previous Trek, but in the worst case scenario, it was a simple mistake.