That's a very good question, and one where I don't really have a definitive answer, as you're the first Steam Deck user I've encountered. Apparently, it is possible to use non-Workshop mods with Steam Deck, but I'd have to know more about the file/folder architecture of a SimCity 4 installation on a Steam Deck in order to even guess at how to pull it off.
TarkusSC4
Alex joined
TarkusSC4 is a modder who has been active in the SimCity 4 community since 2006. He has been a member of the NAM Team, producers of the Network Addon Mod for SC4, since February 2007. He is also an Assistant Adminstrator at SimCity 4 Devotion, one of the largest online SC4 communities.