DEQ2496 - Jitter issue

Surprinsiggly, I found that the DAC 1 was not sounding as good as the analog output of the DEQ.

Then I think you have nothing much to worry about.

Optical has about twice jitter of coaxial but in case of Benchmark suppression is so high that it doesn't matter. Jitter (noise in time domain) creates sidebands at very low level (-80dB typ) but still audible since not harmonically related to root frequency. With complex signal whole bunch of sidebands becomes low level noise (hard to detect since present only when signal is present). Transitions of digital waveform become uncertain (timewise) when in slew rate is low and noise is present (transport, DAC or cable) or when transitions are fast (high slew rate) and signal reflects on impedance boundaries or combination of both.

To minimize it I would use very well shielded digital cable (double or even triple shielded) that is about 1.5m long very well characteristic impedance matched. Shorter cable might bring reflection back on the same transition that caused it affecting threshold point (since limited slewrate) but the longer one will make reflections stronger.
I would try to get good transport and power supply conditioner/filter (I use it in spite of Benchmark DAC1).

Benchmark solves the problem while Bel Canto DAC3 is a little better (according to Stereophile review).

Thank you very much for your contributions. I also own a Benchmark DAC 1. I have tried to connect it behind the DEQ2496, in order to take care of the digital output. Surprinsiggly, I found that the DAC 1 was not sounding as good as the analog output of the DEQ. I need to find a good AES cable to redo this test (I was using an optical output).
My question is related to the benefit, or not, to upgrade the internal clock of the DEQ...

I'd suggest to get something like a Benchmark DAC1 on lone froma guitar or music store and experiment. There are so many variables that it is hard to say whether you have jitter or not. For sure it could be a problem depending on your gear, connection, power etc. Jitter is audible but in most decent modern gear there will not be a "night and day" difference - subtle differences in teh treble or lower midrange more like.

There's a ton of discussion about jitter here an on other audio sites. Do some reading and you will find that it is a controversial topic. After doing quite a bit of reading myself, it is my opinion that the levels of jitter in modern digital gear are largely inaudible and that trying to correct already nominal levels of jitter with devices such as you describe are largely ineffective and/or inaudible as well. Just my two cents, YMMW, etc.