Then it should work, unless you have something in an .htaccess file that's sending js/ or .js to the wrong place, or implementing compression that your browser can't handle.
The JS and CSS are run client-side (on the browser), so nothing else that your server does should affect those files, unless they're not getting to the client in the first place. Is this a Linux/Apache server, or Windows? See if your browser has developers tools to monitor network traffic -- maybe you can confirm that your files are getting over.
Do you have evidence that some or all JS files are not making it over? Can you examine the browser cache? Also try clearing the cache just to make sure it receives a fresh copy of everything.