JBoss AS supports hot deployment - i.e. it picks up new applications from the "deploy" folder when the server is running. Usually, in production this is turned off. But on a development server, this is on. What kind of "effects" are you asking about?
Effects in the sense - in creating work folder and in correct running of overall application.
I dont know about any "particular" effects. So, just wanted to know if at all there will be problem to the application.