Debugging a system like this must very scary because of the tremendous responsibility. It is intersting to know how they actually communicate with it and handle auth.
It might not be authenticated. For some NASA probes, they just figured that any attacker would need control of a global network of high-gain radio antennas, and there aren't very many of those. Physical security at DSN tracking sites is sufficient in most cases.
I wonder if this threat vector will change as more countries become space bound. Curious to see the JPL Security Coding Guidelines, whenever that is written.
AES-256 on both uplink and downlink sides. It's fast enough and the NSA thinks it's good enough. Put a timestamp inside the cleartext to prevent replay attacks and re-key the encryption module every so often to prevent cryptoanalysis from breaking your current key.
