They shouldn't be deleted automatically.
The uninstaller needs to ask the user if he/she wants to remove the config and data files.
Maybe the user will want to install the game later, so preserving config is beneficial.
I don't know yet, @Stan`If they already made it as a mod and are ready to maintain them, it may work out better in the long-run. For me to update everybody's maps that already exist in the mod every time a new version of 0 A.D. is release might be too much at some point. But these are cool maps, indeed.