Wow, the CDJ-2000NXS2 upsamples 48khz to 96khz. I was not expecting that. You should make sure that you're testing 44.1khz files over SPDIF to a 44.1khz digital receiver, and if you're testing 96khz files, make sure the receiver is running at 96khz, too, rather than SRCing any of the digital outs to the analyzers.
The CDJ-3000, by the way, resamples everything to 96khz similar to the way the new Denons do, rather than having any change in the SPDIF rate, but the CDJ-3000 appears to use a better quality interpolation than the new Denons that seem to use a very computationally efficient method. The new Denons use superior key correction, though, but distortion is of course cummulative. If you're not using key correction, the CDJ-3000 should give superior SPDIF output, while if you're using keylock, it starts to get into a matter of taste in some respects. Personally, I still give the overall sound nod to the CDJ-3000 even with key correction, but others disagree with me.
InMusic actually raised the corner frequency of their anti-aliasing filters for the digital audio processing that's happening all the time on the players after we complained about the substantial high frequency roll off in the DSP phase. While they did improve the extension a little, especially on higher rate tracks, they now appear to let in more aliasing and therefore intermodulation distortion plus noise that particularly shows up on frequency sweeps and on a 20-tone IMD test, indicating an IMD 'hump' on complex mid-amplitude material. In contrast, if you run a 2-tone SMPTE IMD test that simulates only more minimalist music, it comes up pretty clean on the new Denons. There's also some ultrasonic grunge still getting through. Personally, I'd rather have more treble roll off than more aliasing, and I wish when you turned the B layer (and effects) off you got better quality SRC interpolation since you'd be freeing up available resources. IMO, the current overall sound with lossless on the Denon Prime units is closer to lossy audio files on older models... assuming you're comparing keylock off. Again, if you're doing keylock, that's dominating the distortion and frequency bandwidth changes. Here are some videos of test waveforms:
The last versions of Virtual DJ 7 were actually bit perfect at zero pitch regardless of master tempo being on or off, and while for a while there later versions had some issues, I have been told that their latest versions once again can do that... of course assuming the rest of your system is not SRCing the stream and you don't have VDJ's mixer, effects, and stems separation in the path.
The oldest Pioneer DJ CDJ-2000 were usually bit perfect from their SPDIF at zero pitch regardless of whether keylock was on or off. Their Wolfson DACs weren't too bad, if a bit shimmery. The older pre-InMusic Denon DJ decks tended to have better-sounding DACs, though. I don't think I ever bothered testing the old Denons because they always sounded amazing. I did also test the Gemini MDJ and Hanpin players, though: