Web projects most definitely should just be updated incrementally. Would need to know more.
ESB projects similar, but could be a bug (since its newer code base than the good old Web deploy)
EJB projects - are the files actually not updated in the deployment ? I'll assume they are and the problem you are seeing is that EJB's aren't dynamically reloadable. They require a restart of the module. Maybe the same issue you see for the web projects ?
jbpm projects have their down deployment approach at the moment. Are you using the jbpm deployment tab or copying a .par file or how ?