[Anaraxes]

Skyscraper orientation aligns the gravity direction with the thrust direction. So, if you give the gravity generators sensors (or connect them to the engine controls; either way gives you more stuff to break and thus have to fix to get the gravity under control), you can automatically reduce the gravity as the thrust increases, or even flip the orientation of the gravity vector (if the tech allows) to counter thrust over 1G. If it's naval-ship orientation, with the "rockets" oriented out the "stern", then any significant thrust is going to be a sideways shove on the crew. That's especially bad if that thrust level changes a lot (say, to randomize the ship's vector), or if thrust is high (so the crew couldn't stand up while the ship was thrusting).

Note that on Earth, "naval ship orientation" is really the same as "skyscraper orientation". Both are aligned so that the decks / floors are perpendicular to the predominant direction of gravity ("down"). If you have high thrust that's often used, then the predominant direction is the direction of thrust. So it only makes sense to align the ship to take that into account, even if you have artificial gravity as a supplement. If the ship uses thrust only briefly and spends most of its time coasting, like a modern-day space probe, or has very low thrust, then you might ignore that direction as irrelevant during the mission.

Naval ships are narrow compared to their length for hydrodynamic reasons -- less drag on the hull makes for a faster ship, though they have to keep some width for stability. Skyscraper are tall compared to their width because land in downtown cities is scarce and expensive and bought by area, not volume. (Also ego...) Neither of those factors are relevant in space. You might want a long, pointy ship just for the sake of tradition, but that's not really dictated by the environment. The fact that you have to travel more against gravity in a skyscraper (hence elevators), while you can walk horizontally over more of a ship, is a practical advantage for the ship layout, but it's not a dominant factor. (Besides, elevators are just another fun thing to break, right?)

A sphere gives you the most volume for the area of the hull, and minimizes the travel distance between points inside the ship. (Not that travel is normally random; the architects will no doubt take into account where people have to get to in their jobs when choosing a layout.) Spheres also minimize the moment of inertia, so they can likely more easily change direction than a long, thin object. You don't have to have spherical ships, but other shapes will have a reason for their existence.