Well, one of the more hardware-heavy comic books, Cam Kennedy’s Dark Empire (largely ignored by subsequent stories) had all sorts of ships in the atmosphere, including Star Destroyers.
The Super Star Destroyer Lusankya, sister ship of Vader’s Executor was buried on the capital world of Coruscant, and later left under its own power killing millions of people in the process. So it certainly had no problems traversing the atmosphere.
These are the same people that gave Voyager landing gear…