Hive metastore database details missing in hive-site.xml
JDO details are only applicable to Hive Metastore. So, for security reasons they are not included in client configuration version of hive-site.xml. The settings that you see in Cloudera Manager UI are stored in Cloudera Manager's database. CM retrieves and adds those values dynamically to a special server-side hive-site.xml which it generates before HMS process is started. That file can be seen in configuration directory /var/run/cloudera-scm-agent/process/nnn-hive-HIVEMETASTORE/ on the node running HMS role (with proper permissions; nnn here is an incremental process counter).
By the way, CDH 5.4.6 has been EOL'ed for ages. Why aren't you upgrading?