In the sentence "Whichever way the ebb flowed is where the jolly-boat went," there is 1 noun clause: "whichever way the ebb flowed."
The phrase "is where the jolly-boat went" functions as a predicate, and "where the jolly-boat went" also serves as a noun clause, but it is part of the larger construction initiated by the subject clause. Thus, the answer is: 1.