I've been meaning to get Atomic Edition but I heard somewhere that it doesn't have mouse support? Is that true? How does it compare to today's traditional PC FPS controls?

If you want the usual mouse look control, just use one of the free engines that can run the game files, like eDuke.
The native engine in the DOS game, if I remember correctly, has basic mouse look which is okay but not great. Mouse movement forwards and backwards makes you walk/run either forwards or backwards, but holding a 'look' button down changes it so that the mouse looks around fully.

Press "U" in-game to enable mouselook.

when build came out mouse look was not in wide use so most did not know that build games had mouse look since build cheated at 3d rendering like doom and wolf 3d the look up and down just distort the screen to emulate the angle. the ports use opengl so they have a quake style mouse look.