Fellow ST user here! .prg was the most common extension but .app was certainly used in some cases. I think it denoted a different format.
Weren't .prgs the actual "foreground"-programs while .apps were the small helper tools that ran in the background and stayed resident even if not in focus? I distantly remember some apps getting a spot in the menu bar...
(It's been ages since I touched that system, good times, though.)
The resident tools were .ACC (desktop accessories).