If you have wi-fi enabled on the Kobo I'm not sure there is any pressing need.
However, I never enable wi-fi so I use Kobo Desktop to do the following:
1. The initial login when I first register the device with my email account
2. The initial download of standard dictionaries.
3. When buying a kepub from Kobo, having it download to Kobo Desktop means I can easily use Alf's de-DRM tools on it. Personally I prefer this method to messing around with ADE to get the standard epub format.
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