The ultimate security by obscurity. Do you have a 30m antenna? Can you point it exactly at the space ship with almost no error? Do you know what it's code and protocols are? OK, please reprogram Voyager
Also, that nothing is encrypted but I guess encryption can be broken.
Our way of encrypting things is incredibly basic. We are basically just asking like a toddler: What number am I thinking of? If you guess correctly, congratulation you broke the encryption.
A civilisation just a few decades ahead of us will have no problem breaking even the most modern encryptions. Any advanced Alien race, will look at our way of encryption, like we look at the Caesar-Chiffre or the Enigma-Machine today. Clever for it's time, but no real hurdle for a modern code breaker.