I always thought it was both, i.e. they were speaking in Navajo but the messages were also coded to provide extra security. Am I wrong?
I thought they were using the Navajo language itself as the code. That is why the code-talkers always had bodyguards; the Navajos were the only ones who could understand each other! That info wasn't declassified until only a few years ago so that the US could use it again if need be!