I don't know about a lunar mission, but for the deep space probes, you need a global array of 70m dishes, and the knowledge of exactly where to point them, before you can even have a chance of communicating.
Honestly, I'd be extremely impressed if hackers managed to issue a command to a spacecraft.
Some hobbyists tried to salvage an old NASA probe (with NASA approval): http://spacecollege.org/isee3/ and they were able to fire thrusters once.
I would expect NSA would be already doing what these guys did with regards to receiving data. It’s practice for when they want to do the same with Chinese spy satellites. And, if they want to embarrass China, they could cause a failure by uploading a rogue command. NSA certainly has access to the required dishes.
Honestly, I'd be extremely impressed if hackers managed to issue a command to a spacecraft.
Some hobbyists tried to salvage an old NASA probe (with NASA approval): http://spacecollege.org/isee3/ and they were able to fire thrusters once.