In the novel - which I misremembered the title of; it's The Shakespeare Stealer - the shorthand the boy uses is the idiosyncratic personal invention of the clergyman who taught it to him, and they're the only people who know it.

The author may have been using the old "it was invented early, didn't catch on, and was forgotten by history" trick for the sake of the plot.

And he used a pencil; or rather, a plumbago stylus, pencils as we know them not having been invented yet.