Hi to “all of you” 
First of all, many thanks for your inputs regarding my issue. You got it all right!
I fixed my issues by wrapping the I2S cable with aluminium foil 
.
For the Pro V3 + Dac, I wrapped the whole cable with one piece of foil. No link to any ground or anything else, just a “shield” around the cable and this fixed the issue. The sound is now totally clean.
Regarding the Pro V3 + Spdif output board, wrapping the whole cable with aluminium foil just made it worse… Like if all the mess was stuck in the shield… So I tried to separate the 7 wires from each other and to wrap them in 7 pieces of aluminium foil, again, without linking it to any ground. This made the trick! It now works perfectly without any cracks, clicks, etc.
So the issue is indeed the really bad “shielding” of the I2S cable… Nothing to do with a firmware version or other digital issue… It’s a shame for such a great product, to be stuck with a bad piece of cable… But the fix with some aluminium made it for a few cents!
Let’s play with the multiroom now
Thanks for your help!