Another off the wall idea I had -- I haven't tried applying any of this yet. I'm good at puzzles but not encryption...but when I was a kid, I got into the code stuff quite a bit. When my brother and I were around 10, we (along with all our friends
) got one of those "secret decoder" rings in a box of cornflakes. We used it to exchange notes with our friends about top secret things we didn't want our parents to know about, like getting together to play in the old shed that was considered too dangerous. The ring didn't do anything sophisticated, just a rotating substitution cypher. There was a code that you put at the front of the text so your friend knew which setting to use.
We wrote everything in pig latin first, then encrypted it, so everything ended in the same two letters. Our mother, who is very smart despite only finishing 8th grade, figured it out in nothing flat. So then we went to variations of it. If I recall correctly, the one we eventually came up with that she couldn't figure out was encrypting first, then applying the pig latin, and then breaking it up into arbitrary "words" of varying lengths to make it look like real words, but the spaces didn't mean anything.
I'm wondering whether some similar sort of evolution might apply here. The fact that he started doing this when he was 10 and continued to use suggests that it started as something fairly basic, but he continued to use and work on. If as we suspect he also used abbreviations, shorthand notations, and phonetic spellings as it evolved, it would become a private language, not just an encryption.