FLAC (and ALAC, for that matter) is a lot more computationally intensive to decode than MP3s and AACs are. My guess is that the CDJ's, like all purpose-built embedded devices, has the CPU power to do what it was spec'd to do and not much more. Or it might be a limitation of the RAM it was spec'd with. Or they do all their decoding in an ASIC, and the ASIC doesn't understand FLAC. There are many possible reasons why the hardware won't support FLAC. Sure, I'd prefer if it did as well, but no sense beating the dead horse on this one. (Anyone ever seen a teardown report for a CDJ-2000? I'd be curious just what CPU and memory it does have...)
As to Vince's question about file formats: I have used AAC 320k until recently, and now have been migrating to AIFF for all new music. Both support full tagging, without all the incompatibilities that many WAV taggers have understanding the WAV Broadcast Tag specification. AIFFs are uncompressed, so large, yes. But HDs are so big and cheap these days, that I no longer care about the filesize. Even 64GB flash drives are cheap now (just did a check on Amazon, and the first one listed is $60... $90 if you want a faster one). My AIFFs from Beatport average around 80MB per track. Round up to 100MB to be extra conservative, and a 64GB flash drive would hold over 600 tracks (I'm also leaving a hefty bit of overhead free for the all the metadata/beatgrid/etc info that Rekordbox needs to save in addition to the tracks themselves). That's way more than enough for any single DJ set you might do. And for the mobile folks that need every track in their library in case of special request, an external 1TB drive is also dirt cheap these days and would hold ~10,000 tracks.