If you add a brand new application, you do not have to restart Wowza. If you make a change to an application, it will have to be re-loaded before new connections are affected by the change. You can do that with JConsole. Unloading one application will only affect clients connected to that application, but not others.
You should be able to add or change a VHost configuration similarly.
If you add a jar file to the Wowza lib folder, or make a change to Server.xml, or log4j.properties, you have to restart Wowza to make that change take affect.
Richard