I have read in the past on how the Navajo code talkers were never deciphered by the Japanese. But I'm curious as to what the Japanese thought of the language. Did they suspect it to be a Native American language?
Yes, in 1944 the Japanese military tortured Joe Kieyoomia, a Navajo POW who was captured in the Philippines in 1942, to have him translate the messages. The Navajo code talkers replaced military terms with unrelated, everyday Navajo words, so Kieyoomia was unable to make sense of the messages. The incident suggests that the Japanese knew it was Navajo and were attempting to decode it.
Exactly how they figured out the language was Navajo is still a mystery, but there are a few possibilities. A linguistics expert in Japan might have been familiar enough with the language to identify it, but not enough to translate it. There were also a few security leaks, such as an article in the Arizona Highways that talked about the Navajo code talkers. The code talkers also started their messages with the indicator "Arizona" or "New Mexico," which might have clued in the Japanese.
Source: Huffman, Stephen. "The Navajo code talkers: a cryptologic and linguistic perspective." Cryptologia 24.4 (2000): 289-320.