We're used to a very rational way of thinking, whereby one would devise a system and apply consistently throughout the whole text, but from what little I have seen and read of this manuscript, it seems that whoever wrote used lots of artistic license and was intentionally trying to conceal the content. So it could be possible that the writer(s) decided to do away with all manners of grammatical rules, and parts of the language, like article, propositions, and the letters F and Z (if that seems weird, imagine that there was no U in Latin). All the other missing letters are not in the Italian alphabet.
Though, it would be interesting to see how this theory works with the non-herbal sections of the manuscript.
Finally, I totally agree with muddylemon that attributing to Da Vinci is silly. Like he was the only literate Italian alive in 15th century.