As a part of one of the recent projects I did some research on this and starting Windchill 11, TDE is supported. TDE encrypts the table spaces and ensure the data at rest is protected. The steps to configure this is detailed in Advanced Deployment Guide for 11
For the JDBC between Oracle and Windchil, i don't see an instruction from PTC to switch to TCPS.- probably provide full connection string in wt.pom.jdbc.host and use wt.pom.dbConnectionPropertiesNameList and wt.pom.dbConnectionPropertiesValueList to pass additional props. Not sure whether this is supported and i have not tested it.