Something to think before get rid of cortex_handler.c and other ARM related files :
The Cortex-M3 processor introduces new powerful features (if compare with prior art). This make the Cortex-M3 processor attractive to existing ARM processor users as well as many new Arduino users considering use of 32-bit micro controllers in their products. Let's consider only NMI_Handler, a non maskarable interrupt for safety-critical tasks. NMI_Handler is the highest priority exception other than reset followed by the HardFault_Handler. It is permanently enabled and has a fixed priority of -2. It's already defined in sam3x8e.h and startup_sam3xa.c. I believe, whoever from Atmel or Arduino added this file to the library, surely was thinking in future developments related to NMI.
A practical application? NMI could be connected to a watchdog timer or a voltage-monitoring block and generates panic requests that warns the processor to take actions if the WDT hangs or when the voltage drops below a certain level. Arduino Due could turn on or toggle a LED through sam_gpio.h. I would even go as far as to write an example. In other words, the fact that is not useful now, doesn't mean that we should cut it out of Arduino library. Remember, we are pulling Due from the ARM underworld to Arduino arenas. I am far to be an ARM connoisseur but just a different point of view.