Academy was originally released on 3.5" HD floppies. I believe that's the only format that was available in stores, though it's possible some 5.25" HD copies shipped. The only CD versions of Academy are re-releases -- ones that came in collections of games or the later EA CLassic release.
Armada was released on CD and 3.5" floppy disks on the same day - there's no difference between the two versions.