That's really the point. We know why it was really done... for the same reason that so many other nonsensical design decisions have been made through the years... "Becuz it'll be kewl!" But is there any plausible technical reason for doing so?
There is no reason for the nacelles to move. It seems to slow the ship to get the engines up to the proper place. Also when you have moving parts things will break that is just a fact.
If you were doing it because it was cool then make it as cool as you can. I would love to see the nacelles in the down position for low speeds and have them move up for faster speeds. You could throw in some BS about warp bubbles, saving sub space or something so there is a weak reason. I personally have never liked how Voyager looked with the engines in the up position. I would of love to see the ship with the engines in a permanent down position so it looks different then all of the other hero (expect Defiant) ships in Star Trek.