The two DACs I have owned in recent years -- the PS Audio Perfect Wave and the Northstar 192 -- both have BNC inputs. I always assumed those BNC inputs were included because BNC digital outs are more common on European transports than they are on US transports. For most digital transports made for the US market, the only outputs I ever run across are S/PDIF and Optical.
I have tried connecting my digital transport, the Perfect Wave Transport, to my Perfect Wave DAC using a BNC and an RCA digital cable. The two digital cables were from the same manufacturer. I could not tell any difference in sound quality between BNC and RCA.