This is not an error message. Rather it warns you that if you are going to configure the server farm then those services will be restarted. But, you need to check if there is any application running in IIS. Because, if you restart the IIS, Application Pools and Timer Services then some applications will not be available for some time (till IIS, App Pools and Timer Jobs getting restarted). There is no foolish question, there is no final answer...