@eabreu savapage-nfc-reader uses Linux package libacsccid1 which is a PC/SC driver for ACS USB CCID smart card readers.
There are PC/SC driver packages for other smart card readers available, but I do not see a PC/SC driver for HID Proximity Card II readers in Linux (Debian).
HID Global does have Linux PC/SC HID OMNIKEY drivers available for download, but I have no experience with this solution and don’t know if this suits your requirement.
Finding out if/how this HID solution works will surely need substantial research. A first step would be to get plain RFID reading going in a proof-of-concept setting with target reader and sample card(s). Next, the proof-of-concept needs to be integrated into savapage-nfc-reader.
May be you can get support via the PCSC lite project to find out about HID support. I hope this helps you to get on your way.