I thought the same years ago when I read a book or two about the history of this book (one was great and scholarly, the other was too sensationalist)

It's a very famous story and book (definitely the most famous medieval book with ciphered text and weird drawings.. if that's really a cipher hidden behind a code that even computers broke their teeth on and not pure gibberish. A great deal of experts believe it's the obsessive work of a schizophrenic monk (or illuminator) - pointing out all the similarities between it and art made by the insane, not the ciphered work of a scholar with any hidden meaning - the legends long assigned authorship to Bacon, or to Elizabeth's astrologue).

I wouldn't be surprised Jordan came upon it, though there are several other examples of medieval scholars who have used a cipher for their notes to pick from. Jordan was most likely not really versed in the topic, though (which makes the possibility he was inspired by something really famous like this manuscript more likely). He constantly mixed up the terms cipher and code in the series. Hidding information in descriptions and notes about flowers is using a code (Verin must have assigned secret meanings to words and such, so she can write down notes about something else in plain sight). Using a cipher on the go, and hide it in a coherent text about flowers would be terribly impractical and difficult, requiring a lot of forethought about the botanical text and quite unsuited for casual notetaking about the BA.