I'm not used to these systems, so can't give you much help. Maybe someone else reading this can, but it's probably better if you ask at a Citrix, or MS, related support forum. But what is exactly the problem?
- The PDF-ShellTools integration in the Windows Shell is provided by a custom DLL Shell extension, that provides a in-process server for each of the handlers (right-click menu handler, drop handler, properties handler, etc.).
- PDF-ShellTools must be installed, and registered in the Windows registry, by user.
- The command line interface acts as a stand alone application, even if the Shell extensions aren't registered.
If you can deploy, in such a system, a tool as the well known WinZip, and have its Shell integration functionalities at the clients, then the same can be done with PDF-ShellTools.