It ignores the request because your RewriteCond pattern matches index.php only without parameters attached in the URL request.
I would NOT strip out parameters. If you do anything, do this:
- Link to the URL
www.example.com/emulators/Atari from the pages of your site and set up an internal rewrite to fetch content from the path
- Set up a redirect that triggers only on external URL requests for
www.example.com/emulators/index.php?folder=Atari and redirects to