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Wrapping up my comment as an answer: Imagine you’re a Japanese cryptanalyst in the year 1944. There is no such thing yet called “television”, and you’re still decades away from a wordwide network feeding you with all the knowledge you could wish for. In that case there’s only a minimal chance you’ve ever heard or seen a Navajo. So, you’ll be wondering ...


I think that in a completely unknown language you have to do frequency analysis on whole words and match that against English. I believe they just didn't have the word-level stats for English, in the military context, and I guess they did not have enough material to derive any significant stats from.


If you combine two affine ciphers, you obtain one affine cipher. Say the first cipher is $e_1(x) = a_1x+b_1$ and the second is $e_2(x) = a_2x+b_2$. Then $e_1(e_2(x)) = a_1(a_2x+b_2)+b_1 = (a_1a_2)x+(a_1b_2+b_1)$. Note that if $a_1$ and $a_2$ are both relatively prime with the modulus, then so is $a_1a_2$, so the new cipher can also be deciphered.

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