Hey it's thanksgiving and I'm a little drunk. Apologies for any errors.
Keep in mind that "encryption" bundles together four different concepts: confidentiality, data integrity, authentication, and non-repudiation. To successfully do space science, data integrity is suuuuuuuuper important. Like if you send a command to the spacecraft to fire the engines for (binary) 000000010110010 milliseconds, and a cosmic ray happens and the spacecraft receives a command to fire the engines for 001110010110010 milliseconds, congratulations, your mission is totally fucked. Voyager was launched with Reed Soloman error correction before fundamental cryptography fundamentals like DES, DH or RSA were published.
Confidentiality is kind of a non-issue with spacecraft. If ground control says, "Fire the thrusters for 174 seconds, authentication code 0x8d0a8fc7" or whatever there are no secrets. Non-repudiation is also a non-issue: NASA doesn't need to prove to NASA that it never sent the self destruct command. NASA already knows what commands it sent.
Authentication is the bit that prevents unauthorized commands, and honestly, the authentication tech is not that complicated. We need 128 bit keys (or 256 if you're paranoid) to do confidentiality correctly, but we use 64 bit keys with "known broken" algorithms like MD5 to do authentication, and that's known to be totally safe.
So of the four pillars of encryption, one of them had to be built in from day 1, or you'd never accomplish anything. One of them is kinda of an easy problem actually, even with old technology. The other two aren't part of the attack surface.
Spacecraft also have a HUGE advantage built in: shared secrets. Ground control can program a secret key into the spacecraft before it's launched. After it's flying around you can leverage stuff off of that shared secret to authenticate communications. This totally sidesteps all of the hard parts of TLS, which involve certificate authorities, certificate revocation lists, etc.