Documentation and logs of the Voyager and Apollo projects are public, comprehensive, and fascinating reading. They do use authentication and keep the keys secret. They are literally rocket scientists.
The techniques were probably closely held at the time to prevent Soviet interference, but these days you can just download the circuit diagram PDFs.
[0] Simulated, since the owner of the original AGC wanted it back.
Can you link to the documentation for the authentication mechanism?
Literally they are not. The rockets used to launch the Voyagers were built by Martin and General Dynamics.
"from the beginning" doesn't really mean much of anything, and the system would need to be pretty sophisticated just to work, even if 100% of the users were operating in good faith 100% of the time.
I'd say that it almost certain that by the time Voyager was launched, there would have been robust authentication just out of necessity. By that time they'd have decades of experience dealing with software bugs, to say nothing of bad actors.