The annotations only provide default values. They simply make deployment descriptors optional.
As far as I know you should still be able to override the values in the service-ref descriptor of the web.xml for servlet clients and the ejb-jar.xml for EJB clients.
However most modifications to the WSDL will require you to regenerate the client stub anyway. So the only thing about the referenced WSDL that really is configurable is the endpoint URL. And the WSDL referenced is often stored inside the WAR or EAR anyway (i.e. it's a copy of the original WSDL).