The window manager learns about a client's PID because the client tells it about it.
For example, when I run the following command and click on a random window, I get:
$ xprop _NET_WM_PID
_NET_WM_PID(CARDINAL) = 5242
However, it seems like Xpdf does net set the _NET_WM_PID property. There is nothing that a window manager can do about this.
Sorry.
(xprop without any arguments gives you a complete list of all the properties that a window has. It looks like xpdf does not set many properties on its windows.)