1 https://mashable.com/article/nasa-space-shuttle-secret-spy-s...
2 https://en.wikipedia.org/wiki/Nancy_Grace_Roman_Space_Telesc...
There were a number of classified space shuttle activities.
For example https://en.m.wikipedia.org/wiki/STS-51-C
The cargo retrieval potential was also suspect. Nukes are the one thing that could never be de-orbited into the atmosphere. Shuttle looked like something that could enable nuke weaponry in orbit.
Newer ICBMs are actually orbital, so they don't have to go so high and thus be visible over the horizon to radar. But they obviously deorbit after less than half an orbit. It also enables them to get to the target in much, much less time.
I have read in several places that one of the USAF's requests, re the dimensions of the Shuttle's Cargo Bay, was that it be big enough to hold a Delta upper stage (I think technically called an Altair) and payload.
The idea was that the Shuttle would take the upper stage and payload to LEO, and then the Altair would boost it into GEO (or trans-lunar) orbit. No need to jettison a payload fairing.
Supposedly NASA eventually won and quashed the idea, since it involved putting a non-man-rated upper stage into the cargo bay of a manned craft. And as far as I know, nothing more powerful than some maneuvering rockets was ever carried in in the Cargo Bay.