you're thinking inside of the box, applying our limited knowledge of flight to a people, if they exist, who have a far more advanced form of propulsion, and flying.
Face it, planes and rockets can't get us from one solar system to another. If they can do it, then their technology is waaaaaay…. beyond ours.
Aerodynamics as we know it, only applies if you have to deal with air friction and gravity, thus, the shapes of our planes and rockets.
If you can negate gravity and/or destabilize matter around your ship, it doesn't have to 'slice' through anything and can be in any shape whatsoever.
A cylindrical shape would be an excellent use of an enclosed space allowing a greater square footage on every round level than any other shape. (Work out the math yourself. Circles rule in square footage)
Strategically, if you are examining a planet for whatever reason, you would send down a variety of different ships for various purposes. Small scouts to zip around looking for places of interest, and bigger ones filled with equipment or possibly for extensive specimen collection. In that case, cylindrical shaped ships would be ideal.