I recommended this app to a friend of mine, that isn't an advanced user, and he managed to delete something from the windows folder (I think) and had to reinstall windows afterwards.
A checkbox in the install screens of the app would be great, so I can ask other people to be very cautious when installing and to check it, and so the protected & hidden files won't be present in the search results.
Also, this kind of checkbox would make newcommers to your app more aware of what they can do with your app, and decide for themselves if they want to check it or not. Only a ''hidden'' option in the app's menu I believe isn't the best idea.