Indeed. Even in tight spots that might require a quick warp getaway, Janeway keeps the nacelles down at impulse. Which sort of suggests that nacelles down is the ideal way to rapidly launch to warp.
Which in turn would support the theory that it's not the position that's important, it's the movement. Perhaps you get better acceleration when you flap the nacelles than when you keep them up all the time.
Sometimes it's claimed that this would be the first or perhaps only class of Starfleet starship that can land. However, this was never suggested let alone confirmed on screen. All we saw was that no other starship landed and survived to tell about it. It is theoretically possible that landing is difficult to do and only done by Intrepid
class or similar vessels, and that some unique technological solutions are required, among these the oddly swinging nacelles. But as said, this doesn't explain the nacelle movement while in empty space...