The story is great, but there are many inconsistencies. I believe it was decorated to the point the facts were bent to follow the story.
After reading the article, I thought that reasearchers learned about the existence of Ajami just recently, far after the colonial powers were gone. That's not true. In 1970, a museum was created in Tombouctou for collecting the documents in Arabic and Ajami. https://en.wikipedia.org/wiki/Timbuktu_Manuscripts (The French Wikipedia mentions "Ajami" for these manuscript, the English page only mentions "Arabic and local languages"). And there have been research publications about Adjami texts for many decades.
> we’ve been told that these people are illiterate, [...]
> their authors were code-switching throughout the text: writing in strict Arabic and in its modified Ajami form.
The article claims the colonial system ignored the local writing system, so it thought that people were illiterate. But Arabic was well-known, and nobody would have tagged "illiterate" on someone that could write Arabic texts.
> [The Mouride] were communicating messages that the French could not understand.
I don't think the colonial authorities were stupid to the point of not realizing that a text written with an Arabic alphabet was not a text. I think anyone seeing this would have thought of Arabic. And anyway it's obviously a text, and the authorities would have found someone to translate it: there were scores of people who worked for the authorities.
Overall, this article could have been a nice and informative story, but it's half PR bullshit, so I had to suppose anything int it was a lie until cross-checked.