I've always wondered why the Japanese didn't do the same thing in reverse. There's gotta be some tiny languages from small ethnic groups on the islands. At the time, it's not like we could have gone and looked up the words in a dictionary somehow. Even without it being encoded, it would have worked pretty well. And yet they didn't even think about it, as far as I know.
Japan is (and was) a pretty ethnically homogeneous place; the largest indigenous minorities are the Ryukyuans and the Ainu. The Ryukyuan languages aren't all that different from Japanese in the first place, and the Ainu were subjected to forced assimilation that has made many ethnic Ainu unable to speak the language, and while I'm not sure of the speaker count in the 1940s, I doubt it was that high. While their imperial possessions at the time would have included lots of other ethnicities, incorporating Korean or Chinese code talkers wouldn't have been that helpful (not that hard to find people who speak those languages), and the size of their Pacific Island groups would have likely struggled to produce enough adequate code talkers. Although the institutional racism of the country was probably enough to forestall any plans in the first place.
It's also worth pointing out why the use of Navajo code talkers was so successful. Part of that is that it's from a language family that was poorly known by linguists at the time. But even within that language family, Navajo is pretty different (compare how different English is from other Germanic languages, or indeed most Indo-European languages). It's also a fiendishly complex language; like, there's no regular verbs--that would make attempts to crack it via standard cryptanalytic techniques rather more difficult. (Also worth pointing out, it was a code within Navajo so that even when the Japanese pressed a Navajo POW into translating the messages, they couldn't crack it).
Apparently they did: I've heard it claimed there was at least one submarine that used Kagoshima-ben, a famously impenetrable dialect spoken in southern Kyushu, for precisely this purpose. I can't find any reliable source though.
More generally though, Japan now and Imperial Japan in particular was very big on there being "one Japan" with one Japanese people and one standard language. Dialects were not encouraged and Okinawan, which is really a different language, was ruthlessly suppressed (kids punished for speaking it in school etc).
Those letters mean: "Welsh not". Back in the day, Welsh children would be punished for speaking Welsh (instead of English) and made to wear a wooden board with WN on it around their neck. The board would be passed on through the day to the final transgressor who would receive a thrashing or similar punishment. Generally all of them would get a thrashing anyway - it was good for them!
Edit: Not, not no ie WN: "Welsh not". Small but important difference.
Context is an interesting key here, I think. That point in the US coincided with a increased interest in First Nations, and in some places a renewed attempt to preserve their heritages, especially linguistically. The US generally sees itself as a nation of immigrants and one axis of its "Freedom of Speech" has historically seen the usefulness to speak one's own language, whatever it may be. Diversity of languages has been a goal for the US at various times in its cultural history. In that context, "what's the most diverse language that Americans speak?" is a question you can ask, and an answer you can find without much difficulty.
Japan had one and only one national language. Japan didn't have the culture of thinking of itself as a melting pot where many languages might meet. It probably wouldn't have thought to ask that question at all "what's the most diverse language that the Japanese speak?" In practice, we can assume that's also why it confused the Japanese for so long in the war, it wasn't a question to think of themselves, it probably was a hard question to ask of Americans if they saw "English" as the national language they might also not think to ask "what other languages do Americans speak?" or maybe even "why isn't this English or a derivative of/code for English?"
While Japan indeed has only one national language, in practice it has many different dialects of that language which are not very mutually intelligible. I live here, any my girlfriend says she can't understand lots of people from various more-remote places. She can't even understand people from the opposite side of her own prefecture. So people frequently have to switch to the standard "Tokyo dialect" when talking to people from other parts of the country. Of course, this is probably lessening over time with mass communications, similar to how Americans largely speak with a "midwestern" or "Chicago" dialect used commonly on TV.
Oh no it's very hard. You go to NYC and spend weeks in barber shops and ethnic restaurants until you hear the fragments of the nearly extinct tongue. Name the language and it is likely spoken in the five boroughs.
A buddy from Latin America who barely spoke English moves to the US. Specifically, he moves to Bushwick, Brooklyn, NYC. He goes, "They all say, 'You gotta learn English. This is America!' but I can't understand any of them - even the Puerto Ricans." First thought in my head was 'dude, you're learning English on hard mode'.
Ranking individual things as more or less diverse than other things is a gross abuse of the concept of diversity anyway. But yeah cataloging the set languages spoken in the US is likely impossible in any meaningful way.
There is a small population of Ainu living in far east of modern Russia. This can be probably extrapolated to them living there during USSR times. Ainu have had... strained relationship with Japan, so they could had been enlisted by the USSR during the war to decrypt messages. That's not to say that Ainu people's relationship with USSR has been ideal either, but them serving as translators during the war seems plausible.
There were footnotes I've seen on Navajo topics that they tried Satsuma(Kagoshima) dialect for the same purpose, but there were no shortages of speakers at the Allied side and the use ended quickly.
Uniqueness of Navajo and other Native American languages was that they were all complete multi millennia isolate from English thanks to how USA came to be. Japan wasn't like that so dialects aren't divergent enough for this use case. Ainu might be a candidate but it's way too high profile.