Hi - it's an ineresting idea. Up to now I have just relied upon people putting only things that they want to treat as scripts inside the script folder. I can see your rationale for wanting to hide administrative stuff like version control artifacts.
FastScripts could also respect the "hidden" flag on a file but I see that it doesn't do that either.
I don't have a solution for this unfortunately, but I will keep it in mind as a possible enhancement for a future update.