Unless you're trying to include php code from an outside domain or via a http URL, then allow_url_include being off should not affect anything. My PHP includes all work and I have both allow_url_include and allow_url_fopen set to off, on purpose.
I have three php include statements on my main page (one includes another php file, one is a .htm file and another is a .txt file).
PHP Code:
<?php include "php/count.php" ?>