Just studied the service manual for the CDJ-2000. So the hold up to FLAC is either the custom TI DSP is responsible for decoding files and its not re programmable (Can't find any info on the chip so its most likely a custom job for Pioneer). If the DSP does not do the decoding then its the amount of code that can be held on the flash memory. They use a 64Mb/32Mb chip, when in mirror mode that gives it 4MB of storage 8MB at the most. While there is a chip for every function, meaning very little code needs to be written to make the CDJ work, I do see the hold up. The space available on the flash memory might be an issue plus converting FLAC API libraries to run on a RISC CPU and integrate to the UI is a considerable amount of work. I can see why Pioneer might not want to dive in that deep. Though for the sake of pushing the industry forward I wish they would.
Unfortunate because the parts used are not forward thinking at all especially with today's FPGA's, but what they used is probably reliable and familiar to the engineers at Pioneer.
Also interesting to note 1)the DAC can run up to 192Khz, 2)there is support for LST chunks for WAV files meaning you can have basic tags for WAV's. I'm going to try writing these tags and test it out later tonight.