I don't know if linking external websites is allowed in the forums, but... I think GOG players can just use this:
http://steamworkshopdownloader.com/ (Steam Workshop Downloader) to manually sync their mods with Steam players.
I've used it to install Workshop Skyrim mods via Nexus Mod Manager and it works like a charm. Problem solved, I guess?
Nonetheless, I'm still deciding where to buy the game. I'll probably get it on GOG, but that's just because of personal preference in their business policies.