Not necessarily, depends on how the ship is propelled in space who knows exactly how it would have to manipulate magnetic or other fields, the shape could be very important for a drive that relies on something other than "throw stuff out the back really fast"
Although i suspect such a delicate drive may fail when shoved into the massive mix of fields around a planet.
Although aliens that have developed FTL travel and the ability to pass through solid matter without disturbing it (it much pass through the air molecules as otherwise when it accelerated to these massive speeds it would produce one hell of a boom) probably wouldn't have to enter the atmosphere to do anything, and if they did would more than likley be completely invisible*.
*again if this is done through the same technology we're currently looking at for bending EM radiation around an object through specially designed materials the shape would be very important
