What is often overlooked is that screened ethernet cables plus RJ45 plugs with metal shield can create a ground loop, as the screen/shield is usually connected to the ground of a device.
Very true. I do have S/FTP Cat6 cables myself –– extremely useful in EM-noisy environments, and when you have to pull an Ethernet cable next to mains wiring –– but as I rarely use them, I hadn't thought about that.
Same potential issue with a USB isolator if the shield is connected on both sides, which is rarely not the case.
In the USB isolators I have, the shield is connected to the local ground (I believe via a capacitor and a resistor in parallel in one.
Unlike Ethernet (especially MagJacks with the built-in transformers), where only the signals (pairs) are isolated, in the USB isolators using the dedicated chips there is no common ground plane at all: upstream and downstream have their separate isolated ground planes, bridged only by the isolator chip and the isolated DC-DC converter. This means that the USB cable having shield connected to ground pin is perfectly okay. (This is also clearly indicated in the datasheet Applications Information, so it is very unlikely that even the cheapest isolators get this wrong.)
A possible issue I can see, however, is if the isolator has a metal chassis, and the USB connectors' shells touch that chassis. It would completely defeat the entire isolation.
There are USB 3.x SuperSpeed isolator chips, like
Advanced Photonics' APISU30/31, APISLCU30/31, but I haven't yet had access to any (
expensive!). At least the APIS ones also need an USB 2.0 ADuM3165/3166/4165/4166/ISOUSB211 isolator for full USB support, too.