There is a difference - size. This could also mean a potential performance difference.
The GO is designed to be a mobile drive, hence the smaller (2.5") disk inside, whereas the DESK is meant to, well, stay on a desk, hence the larger (3.5") disk inside of that.
The 2.5" / 3.5" just refers to the size of the platters inside of the drive itself, often smaller drives spin slower and so performance is less, although for an external drive (presumably storage drive?) it doesn't really matter.
So, do you need portability? If so, get the GO, as it probably won't require an external power brick and just two USB ports.
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