Casey Karst announces that Polybase supports Hadoop RPC protection:
Supporting this configuration allows PolyBase to connect and query Hadoop clusters that have wire encryption turned on. This enables a secure connection between Hadoop and SQL Server; as well as, among the Hadoop Data Nodes.
To connect to a Hadoop cluster with the hadoop.rpc.protection set to privacy or integrity, you will need to alter the core-site.xml file that is installed with PolyBase. This file is generally found at C:\Program Files\Microsoft SQL Server\MSSQL13.MSSQLSERVER\MSSQL\Binn\Polybase\Hadoop\conf.
That’s good news for Polybase users.