I don't think I understand the USB noise bit very well. How does the USB not transfer noise into something like the Singxer SU-1 when USB is being used to send data to it? If it does, and the noise gets removed in the Singxer, why can't that same function happen inside the Yggy eliminating the need of a DDC in between?
It can.
Just a question of how much focus the designer wants to put on that particular issue - in this case, and particularly where Yggdrasil is so aggressive in terms of price/performance, it's easier to say "use a different input" rather than up the cost by doing heroic things on the USB input that simply won't be used by everyone.
Also, you're still largely stuck with the electrical noise generated by the USB receiver circuitry (which is a lot more complicated than an AES or S/PDIF receiver) inside the DAC anyway. So unless you perform some actual electrical isolation on the USB input side of things after it's received by the DAC (which can be done with transformers or optical isolation), then there's only so much you can achieve anyway.
A properly isolated S/PDIF or AES connection (per spec, they're both supposed to be electrically isolated at the source-end but often aren't in the consumer space ... e.g. most "Sound Cards" that have COAX S/PDIF outputs) fixes those issues.
Of course, now you have to care about clocking (which you can largely forget about in USB Audio as there's no sample-clock in the USB Audio stream), but most good DACs, including Yggdrasil, make that largely moot.