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.