Hi,
I'm not sure if /category/ and /category/index.php are considered two urls for seo, but there is a good chance that it will effect them, one way or another. There is nothing wrong with making a quick change just to be sure.
A few thoughts:
URLs
Rather than adding /index.php, you will be better off making it so there is no index.php on any of them, since the keyword 'index' is probably not what you want.
You can make a script that will check if the URL of the current page ends in index.php and remove it, then forward to the resulting URL.
For example, on one of my sites, I require the 'www.' for my domain (www.domain.com and domain.com are considered two URLs for search purposes, though not always), so I have a script that checks each page and if there is no www., it ads it, and forwards.
if (APPLICATION_LIVE) {
if ( (strtolower($_SERVER["HTTP_HOST"]) != "www.domain.com") ) {
header("HTTP/1.1 301 Moved Permanently"); // Recognized by search engines and may count the link toward the correct URL...
header("Location: " . 'www.domain.com/'.$_SERVER["REQUEST_URI"] );
exit();
}
}
You could mode that to do what you need.
That way, if a crawler visits the wrong URL, it will be notified that it was replaced with the correct URL. If a person visits the wrong URL, they will be forwarded to the correct URL (most won't notice), and then if they copy the url from the browser to send someone or link to that page, they will end up linking to the correct url for that page.
LINKING URLS
They way other pages link to your pages is more important for seo. Make sure all your in-site links use the proper URL (without /index.php), and that if you have a 'link to this page' feature, it doesn't include the /index.php part. You can't control how everyone links to you, but you can take some control over it, like with the script in item 1.
URL ROUTING
You may also want to consider using some sort of framework or stand-alone URL rerouting scheme. It could make it so there were more keywords, etc.
See here for an example: http://docs.kohanaphp.com/general/routing