It sounds like there may be a hardware issue with your SMS-200. Is the behavior the same if you bypass the SMS-200 Ultra and connect your Accuphase directly to the Core? Similarly, if you connect another endpoint out of the SMS-200, do you still hear the background noise?
What if you disconnect the Ethernet cable from the SMS-200 and not have it communicate with the Roon Core does it still make the pops and clicks?