Imagine you have a RFID reader ASIC that can deliver interrupts at certain events (like transmit timeouts, FIFO watermarks, ...) like the CL RC632. Imagine, you have a USB-attached micro-controller with an IRQ input, like the 89C5122. Now why in god's name would you _NOT_ connect the IRQ output pin of one chip with the IRQ input pin of the other?
That would be too good for this world. The device would be able to signal the interrupt on an USB interrupt endpoint, just like we all know and love.
But there goes the hardware vendor (Omnikey in this case). He doesn't connect those two pins (though there is plenty of space on the PCB, and therefore the driver has to poll the ASIC's status registers all the time. *sigh*.
If the RFID stack (now called librfid) is finished and I still get upset enough about this broken hardware design, I'll connect the two pins myself and use FLIP to flash a different firmware image into the 89C5122.