I could use a little help from the librarian hive mind! A patron approached me with a book stumper yesterday, and I've had no luck searching on my own. She is looking for a book she checked out from her high school library (so we're looking at a 2011 or earlier publication date) about a boy who works as a spy and joins Shakespeare's play company. It was historical & spy fiction without any magical elements, and she remembers a section at the back of the book with spy codes. She insists this book was not from Gary Blackwood's Shakespeare Stealer series. 

Some other details she believes she remembers: