It's actually very common in our own society for children to make up "secret codes" for their own use or to communicate with a single friend, and notation systems limited to a small affinity group are fairly common even in societies like ours where they have to compete with a standard written language: baseball game records, knitting notation, cross-stitch notation, chess notations, mechanical dimensioning and tolerancing, electronic schematics, shorthands, cement chemist notation, Perl, hobo signs, and so on. If you've ever worked in a company that is more than a few years old, even something as small as a diner, you can probably think of two or three notational systems used only within that company. In our society, at least, it's not just highly neurodivergent people.

I don't agree that being literate in a writing system nobody else uses is equivalent to not being literate.