It wasn't just Navajo. It was also encrypted/coded in Navajo to make it even more complicated on top of an already complex language. The code talkers were incredibly important to the war effort. The code was never cracked either. Makes me really proud of them for doing such a good (and dangerous) job.
Also doesn't help that Navajo is an INCREDIBLY divergent language compared to basically everything else, even other languages native to North America save those of related languages.
It's probably as close to a natlang ithkuil as linguistic science may have ever discovered, so acquiring it non-natively is A TON of work.
Also I may be confusing it with another indigenous language but IIRC there are some Navajo nation communities in which teaching the language to outsiders is seen as a GRAVE offense.
You can guess that the course on Duolingo isn't exactly regarded as on par with their French and Spanish courses. That and their attempt at Hawaiian and the ensuant backlash over how bad both were are partially responsible for why Duolingo has yet to expand into a significant number of new languages.