To work with Smartcards from your AppV you need Local Interaction Allowed set to true. Normally it is not possible for an application in the bubble to communicate with the hardware connected to the system.
Edit your OSD(s) for the application, and past the following code between the brackets if that already exists.
<SOFTPKG> <IMPLEMENTATION> <VIRTUALENV> <POLICIES> <LOCAL_INTERACTION_ALLOWED>TRUE</LOCAL_INTERACTION_ALLOWED> </POLICIES> </VIRTUALENV> </IMPLEMENTATION> </SOFTPKG>
After this test your application, and make sure it works fine.