It seems like you are asking about compound indexes in mongodb. Compound indexes allow you to create a single index on multiple fields in a document. By creating compound indexes you can make these large/complex queries while still using an index.
On a more general note, if you create a basic index on a field that is highly selective, your search can end up being very quick. Using your example, if you had an index on author, the query engine would use that index to find all the entries where author == "John Doe". Presumably there are not that many books with that specific author relative to the number of books in the entire collection. So, even if the rest of your query is fairly complex, it is only evaluated over those few documents with the matching author. Thus, by structuring your indexes properly you can get a significant performance gain without having to have any complex indexes.