So one advantage may be, if you have a lot of javascript code in your header, and use includes () it would GREATLY cut down the amount of code the spiders have to search through before it gets to your copy?
Actually if you have alot of JavaScript and put it in an include file, it will still be displayed in the html because remember that the server assembles all the code in the include into the page being viewed.
To keep lengthly JavaScript or CSS from appearing in the html of a page, you need to place these in their own files and then call for them. In the page you see in the browser, it would look like this to a spider and humans:
<link rel="stylesheet" type="text/css" href="text.css">
<script src="scripts/rollover.js" type="text/javascript"></script>
<script src="scripts/results_popup.js" type="text/javascript"></script>
<script src="scripts/certify.js" type="text/javascript"></script>
This example is taken from our site. The page calls for these things and then it all works in a browser but there is not all this lengthy code added to the html. An include is just that - a separate file that "Includes" its contents onto the page that calls for it.