Although the particular modifications were not used, the Shuttle (as a launch system) certainly was used by the military or at least the NRO. Several missions were classified, most were presumably spy satellite launch and maintenance.

It caused a lot of communication problems because everything was coded, astronauts forgot what code words meant and the whole thing was a bit of a joke.

http://www.airspacemag.com/space/secret-space-shuttles-35318...