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I'm also having a problem with my WD 500gb passport usb 3.0 hdd, it works sometimes but say when the system goes from one application to another it will sometime freeze or hang, and sometimes not even show the hdd. but not sure if it's a built in power save option on the hdd or something.
It may come from the same issue that's plaguing my Wii U.
On the NOA Support page they suggest using an HDD with a dedicated power source.
Maybe USB 3.0 devices are a little more power hungry than USB 2.0 ones and the current output from the Wii U USB ports is not enough to correctly power external USB HDDs that draw power supply from the USB port itself. So if you plug in a USB 2.0 device, the power is enough to make it work; with USB 3.0 devices, there's not enough juice coming from the USB port and the driver powers up but can't function properly. Thus the problems for the console to operate the HDD.
Unfortunately I don't have a USB 3.0 cradle/USB HDD with external power supply to test my theory and buying a 1TB HDD is not on my current To Do list..