Hey Tachyon, You'll love this. I asked that exact question of Rick Sternbach on this board some time back. Essentially the answer was that the producers wanted something on the ship to move. See the thread here:
That was one idea the was flitted about. Added to that was that the folding nacelles also steamlined the ship's warp envelope to allow for higher sustainable velocities, IIRC.
Yea, Like Tachyon said, "Why not just leave them up then?". This theory would work better if in the show we had seen Voyager using different angles at different speeds.