Actually no, these things pretty much fly in the open, chiefly out of necessity (recovering from bit transmission errors is much more complicated when encrypted, and uses up valuable power as well). Usually you have to know a prefix code to get the probe to listen, a la Dr. Strangelove.
It really is security-through-obscurity. Though that definitely isn't considered safe, a lot of spacecraft (especially deep-space ones) are pretty damn obscure. The true weakest link is the security at the ground station, not some fool with a 40 meter dish.
