The reason why they aren't returned in getKnownHostnames() is because we don't know what they are - they are hashed, and the hostnames can't be extracted. Hashed hostnames were introduced in SSH to make the known_hosts file more secure.
We've modified public SSHFTPPublicKey[] getKnownHostKeys(String hostname) to work for hashed hostnames as well as non-hashed ones. The hostname can be passed in and will return the keys if they exist.