The buccaneers have a book...what is it? Why is it ironic that they cut a black spot out of it? Why does Silver mock the person who curt he black spot?

The book is the Bible.

"The black spot! I thought so," he observed. "Where might you have got the paper? Why, hello! look here, now: this ain't lucky! You've gone and cut this out of a Bible. What fool's cut a Bible?"