The plugin does not support encrypted connections.
Cytoscape does not support encrypted connections directly, but you may be able to create an SSH tunnel from your client machine to the SQL Net port (e.g., 1521) on your Database server. Then you can just use a normal JDBC connection to localhost:1521 which will forward to the DB server.
DBCS user guide for SSH tunnel:
Also, we show an SSH tunnel for Fuseki on DBCS at the end of this blog entry:
Thanks for the two answers! I did some more research on the problem. The cytoscape plugin comes with ojdbc7.jar (at least this applies to the version for Oracel 12.2) and this driver, as delivered, does NOT support encryption. But it can be patched with p19030178_122100_Generic.zip, and then encryption works fine.