Depends on the transport, dac, and cable. The transmission and receiver chips are different for AES/EBU and S/PDIF; that's why the same transport/DCA combo usually sounds a bit different with AES/EBU and S/PDIF.
Which is better - S/PDIF Coaxial or AES/EBU
I have a Moon Nova CDP that I am thinking about using as a transport,which digital output is considered the best way to go, the Nova has a BNC S/PDIF(Coaxial) and AES/EBU(Balanced).The dac that I am considering has a rca coaxial and AES/EBU connection. Thanks for all your suggestions