How do you tell if a script is active?
I have some quest scripting, but that should be self contained (do this once) type of stuff. I have a few variables included in my quests that just serve as bools during dialogues that aren't ever used again. Finally I have a few loose scripts on levers and triggers to do particular things on entering/activating, with a few having tracked ints.
Do you have any OnUpdate() functions running with RegisterOnUpdate or RegisterForSingleUpdate? What are the conditions that keep it updating?
As you can see from that very long thread, scripts still running can be an issue and several people, including myself, have been impacted by failed updates. (If the script is running, Skyrim can't update the script, leaving the mod in a bad state.) I consider Steam worse because people may get an update and not even realize so you can't give them "proper" upgrade procedures. Because of this, I came up with a way to check if scripts could "possibly" be running, and warn the user as needed. It's not perfect or foolproof, but it was better than nothing, imo. (This code is in my ScenicCarriages mod, so in the new update quest code, I check to see if a carriage driver is currently loaded.) Hopefully you won't have to go to that extreme but you know your code best.
I would suggest start testing in your environment and check the log. Try upgrading in an area that you KNOW scripts should be running and see what happens. Then check in an area you think should be safe. If you see errros in your log, then you know you have issues to deal with.