Lots of code could be described as "JEE client applications" - web servers and servlet containers that connect to a JEE server, desktop applications that connect in some fashion to a JEE server, a browser that gets its HTML from a JEE server, a browser that performs XHR REST calls to a JEE server, etc.
JSF only addresses the web layer; it is not suitable for other kinds of clients. So the answer would be no - JSF does not replace all JEE clients. (Personally I'm of the opinion that JSF is not a good choice even for the web layer, but that's a different issue.)
Maybe you can elaborate on what "this problem" is?