The Prometheus has 6 nacelles.
Two on the two main sections and two smaller ones on the saucer. I used to think there were only 5 as well, but someone found me a screencap with the ship separated from behind, there is a second nacelle on the saucers ventral undercut, the part that connects with section 2.
So the saucer does have 2, the one underneath is just hard to see and the two are "over/under" instead of out to the side.
Huh, well there we have it, sometimes even the best of us can miss a nacelle.
Since its a tiny nacelle thats practically hidden even when deployed I think nearly everyone missed it. Like I said it took a fairly large screencap and a bit of squinting to finally see the damn thing.

Its on those Star Trek Files magasine schematics too in its folded up port.