Had the same problem a while ago, the only reason to use a HDD is because of the external power source. Apperantly there is a risk when using A flash drive or HDD without external power where the WiiU cannot provide enough and it will corrupt the medium with read/write errors? I think it is probably linked to the stand by mode and automatic updates, assuming stand by mode puts the machine in a low power state?
But the problem I had is that it is nearly impossible to find a HDD with a small size (both physical and storage wise), as they are only sold/built anymore with desktops in mind with sizes starting at 500GB and up. Making them smaller is actually not economical anymore. And All the small portable ones are for laptops and either have a USB Y cable for extra power, (though I couldnt find one of those either), or just the single USB connection.
This would not have been a problem for me if the WiiU didn't demand the entire drive to be formatted to a filesystem PCs can't use, but nooooo.
So after a while of searching and not being able to update or save, and having to delete and reinstall games on my pityfull 8GB (but really only 4GB usable) WiiU I was like, ah fuck it, and bought a 16GB flash drive of a respectable brand with good read/write speeds. Up until now It works fine, but then again, I am not a power user, and only play the occasional MK8 and splatoon match these days. Still, the whole thing annoyed me way more than it should have and I try to keep all the SAVE data on WiiU. The WiiU is probably my least favorite gaming system I ever owned by now, and the 3Ds my favorite ><.
Ever since I got a WiiU gamecube adapter and found out I can use it on PC I've been hooked on the dolphin emulator playing my GC games in HD, not just wind waker.
BTW, dont get fooled by the whole solid dtate memory has a finite read and write count, though based on truth, that number is so high these days the user wil probably not reach it in his lifetime, but HDDs also wear and tear, and often have mechanical malfunctions before the discs themselves wear out. Build quality is what matters for both. I've had cheap sticks malfunction sure, but burned through a lot more expensive hard drives in my lifetime.