Please try this query to see if there's any data from the Java agent:
GET apm-*/_search
{
  "query": {
    "term": {
      "context.service.agent.name": "java"
    }
  }
}
You can use the "Dev Tools" UI for that in Kibana.
If there is no data coming from the Java agent, there may a problem with the communication between agent and server. There is currently an issue about the setup steps showing connection is successful while it is not. Please try to look for interesting stuff in the agent and APM server logs and let us know if you find anything.
Thanks,
Eyal.