It doesn’t matter if they are “accessible” if there aren’t any links to them (search engines only catalog actually links, and they don’t “guess”), unless these are old urls that you are trying to get out of search engines or something.
If you use the url helpers, like anchor(), then you won’t have to do anything else to clean up your urls once you change $config[‘index_page’] to empty string. It won’t make links with “index.php” in them. However, if you didn’t, and you manually created your anchors using straight up html, then you will have to fix all of those by hand and remove the “index.php”. Hopefully you used the CI anchor() function.
The same goes for images and forms. If you made them by hand instead of using CI’s helpers, you will have to manually fix all of them.