It won't harm anything to add the index.html file to those folders. But, since the .htaccess in some of them completely prohibits access, doing so may be moot, and won't stop the "forbidden" messages.

While I understand your logic, it's also important to note that unless a hacker is absolutely convinced that there's a pot of gold inside worth spending time about, they're gonna move on to another place whose gates aren't so tightly locked. It's not worth their while to stay.