Is the support for the deepsilver/saintsrow.com account coming at some point? I uploaded a few chars back when I still played the game on steam, the menu option to log in to the deepsilver account is missing in gog's version.

I was wondering about that as well. It turns out that the GOG version won't be implemented with My Steelport. To quote IdolNinja of Volition, he said on the forums, "The GOG version does not support online features at all. "

So, you may have to default to the Steam version if you want to upload/download characters.

It is possible to manually migrate character data between SR3 and SR4, even with the GOG version of SR3. I have posted a guide here.