No, tyhere is no difference, the majority of today's separate dacs re-clock the signal as it arrives so unless there are major errors along the way, there will be no difference at all.
Digital Interconnect Questions
I've always used inexpensive consumer grade digital cables of the $25 - $40 variety from Circus City, GoofGuys, etc. I'm talking about the 75ohm coaxial cable for attaching CD transport to DAC. Is there a significant difference in sound quality with higher-end digital interconnects? I've always been skeptical of over priced cables, especially the digital interconnect. I'm not seeking a debate but would like to know if anyone can actually hear a SIGNIFICANT difference. Thanks.