In the book you’re quoting, the sentence is (presumably):
Do you like cheese?
That sentence includes the question mark.
When you quote something like you do here, you use quote marks to identify exactly which words belong to the quote; and then you write, either before or after or in a footnote or somewhere, where you have taken the quote from.
The only thing that should be inside the quote marks is the exact glyphs that you are quoting from the Book of Cheese; i.e.,
“Do you like cheese?”
The attribution that this sentence is to be found in Book of Cheese, book 43, verse 21, is not part of what is written in the book. It is part of the sentence that you are writing. As such, it should not be included in the quote marks that show what words you are copying from the book.
It should thus be:
As it is written: “Do you like cheese?” (Book of Cheese, 43:21).
Side note: it is more customary in English when capitalising titles of books and such things to use title case—where words belonging to closed classes (in English mostly articles, particles, prepositions, conjunctions, and pronouns) are not capitalised—than it is to use start case, where every word is capitalised. That’s why I’ve written Book of Cheese above, rather than Book Of Cheese.