RSA was known by cryptographers in UK communications security years before discovery.

RSA had already been developed by GCHQ (British signals intelligence agency) in 1973, 4 years before it's discovery by the academics.

I wonder what kind of classified scientific knowledge worldwide security agencies have currently that might change the world.

It's an interesting thing to think about in the context of Superintelligence. Perhaps there are secret projects developing them right now.