I have been on the design side of smart card reader/writers for over a decade now and I do not think it would be feasible to modify the Mini 9 to have one internal (other than the existing SIM [smart]card support). There simply is not enough room to do it properly. The closest form factors would be the PCMCIA or USB thumb-drive reader/writers, but again, there is not enough real estate to do it properly in the Mini 9. Now, if the DoD made the change over to contactless smart cards, you could do something in terms of an internal near field wireless reader/writer, which would get the device size down to a usable level, but I do not see that happening any time soon on a large scale in regards to the DoD.
One idea that may work is the new wireless USB device standard which will become more main stream in the coming months. This would allow any compatible USB based device (including self powered compact smart card reader/writers) to securely interface to a standard USB port (which can go internal on the Mini 9) without the need for a cable. So, then you could just keep the reader/writer in your pocket or backpack and use you CAC card "wirelessly" that way. This would also keep your mini 9 looking good since you wouldn't need to make any external mods.