These WARN messages are expected, and they are not based on the required JAR's per Virtual Service basis. The WARN message is a generic message which will appear for all MQ Virtual Services even if it doesn't need the jar files.
The following properties can be applied in the logging.properties for the VSE Service:
This will clear up the VSE logs and just show error messages when something is wrong.
WARN messages about missing jars won't be available.