Yes, USB Audio offers higher bandwidth, hence better digital capability, but that is different from saying coaxial cannot playback DSD files. In fact, 99% of current DSD files are DSD64, only a very small percentage of DSD files are DSD128 and DSD256, so Coaxial output can support a very large proportion of DSD files already. By the time DSD128 become popular, I am sure we'll rectify the USB Audio Problem of N5ii, or we probably will be using N5iii or N5iv by that time.
I think your have confused the clock synchronization of S/PDIF. The clock of Transport (N5ii in this case) and DAC are independent. The Transport will not manage the clock of the DAC, this can only be done when certain Transport and DAC are connect with a special clock link feature that is very rare and only exist in very high end audio equipment. I2S will allow similar clock synchronization function but that is not S/PDIF domain.
Last but not least, the better digital specification of USB Audio does not guarantee better sound performance, in fact, I personally prefer coaxial input of Mojo and Hugo over USB input. I am not familiar with Hugo2 so I can't comment on that. In fact, most DAC using standard off-the-shelf USB receiver solution tends to sound clean and high resolution but less emotional when compare to the coaxial output, and because I prefer slightly warm and full music presentation, so coaxial tends to fit my taste better, but this is personal preference and everyone need to make up their own decision regarding the different digital input of their DAC device.