Pressure, lack of water-specific propulsion, potential rust etc. One could of course argue that this Enterprise was designed to work underwater (hey, they've pulled stupider crap in the movie before so why not go ham?)... except they even have the chief engineer call the captain out on the ship not being designed to go underwater (right before he gets a repeat of the underwater-monster-scare from Episode 1 through the... lesigh... through the Screen WINDOW, if i remember correctly). Actually the plan was always to have them take the Shuttle but that was too costly. Observe how the ship has no landing gears. (The Saucer had landing struts for emergencies but that was never shown on screen and would only have worked for the Saucer alone, which was not easily re-attachable like the Galaxy Class's Saucer would be a hundred years later). They didn't do it that often. I guess they figured out how ridicilous it looked. I HAVE BEEN SUMMONED! To my knowledge there was never a real reason behind it from the initial designers; they moved because they wanted the Voyager to have something distinctive. They were REALLY afraid to put hero ships from other shows or movies into their own contemporaries to avoid "confusion" (you can make your own joke about american TV-culture, they're all good); that's why they couldn't show a Sovereign in the Dominion War (also issues with CGI). Every now and then it would happen (like the Belerophon, an Intrepid Class in Deep Space Nine, or the Enterprise D in These Are The Voyages) but overall they really wanted consumers to imediately have the viewer recognize what show they were watching with a single glance. The moving nacelles were just another gimmick to distinguish the ship more from the Enterprise. Normally someone would come up with an idea as to WHY they're moving, but Voyager, being Voyager, never really did that. Best i can find on that is some noncanon ideas thrown around by Mike Okuda and Rick Sternbach about how the moving nacelles avoid the rupturing of subspace that was discovered to be a direct result of warp travel in one of the later TNG-seasons... except that was found out waaaay too late to change something for the Intrepid Class (the Intrepid itself was probably already doing regular service at that time). Apparently the rupturing isn't so much negated by the position of the nacelles but by their movement during the establishing of the warp field. Personally that's good enough for me but to quote Vegeta: "This is so non-canon it hurts.". However, it would make sense if you think about it as more of a hackjob; take an existing design that's hot off the presses and fiddle with it's components to get a result that's in line with your new understandings, and fix it in any future designs from the start. We don't see many new ship classes after the Intrepid (actually only one, the Prometheus, unless we count the 26th century Monsterprise-J) and with the exception of the Delta Flyer we don't really see moving parts before or after (not counting the moving fins on the JJTrek-Enterprise, but i'm not even going to TRY to figure their shit out. Their ships' nacelles have exhausts at the end. EXHAUSTS.). They probably managed to fix it by designing new Warp Coils, either with hidden moving parts inside the nacelles or by using a new wave-pattern (the warp coils produce little ripples in space, they aren't continuously on during flight. Little ripples can make big waves.). That's the best i can do on the Voyager. Sorry But the tech got a little.... voyagery during Voyager.