This has the N named main character and Elizabeth aspects so maybe this one?

Emma Clemons 

Southfield Public Library

Youth Dept Intern

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: 

• The book had a red cover, and prominently featured the protagonist (potentially holding a sword) -- she described the cover as having a very quintessentially 2000s design. 
• She believes the main character was an orphan, and his name may have started with an N.
• The story takes place in London and Queen Elizabeth plays into the plot somehow.

--