I tried using inputFolder for both [nes] and [atari2600], but neither seemed to do much
The scraping dialog that you start from RetroPie-Setup doesn't read your .ini file to look for folders, but expects the standard RetroPie folder structure.
If you changed the folder in the .ini file, run the scraper manually:
/opt/retropie/supplementary/skyscraper/Skyscraper -p nes -s screenscraper ... other flags ...
EDIT: just to make it easier, you can probably symlink the folders from your SMB mounted drive to the actual RetroPie folders, i.e.
/mount/network/Arcade -> $HOME/RetroPie/roms/arcade
/mount/Consoles/Atari Xyx -> $HOME/RetroPie/roms/atari5200
/mount/Consoles/Nintendo Entertainment System -> $HOME/RetroPie/roms/nes
etc.