Native American Encryption?!

I remember hearing many years ago that one of the branches of the armed aervices during WWII used a native American -- Cherokee? Apache? -- language to communicate. The Japanese (the story goes) went nuts trying to crack the code -- unsuccessfully. Two questions: 1) Can anyone give me a reference for this story (assuming it's true)? 2) If one used a natural language for encryption, and the would-be code crackers did not know it was natural language (say, Hittite), could they crack it? I seem to remember that hieroglyphs were undecipherable until the Rosetta Stone was discovered. But maybe current techniques would do a better job....?