As noted in comments, mixing non-httponly and httponly cookies is not a problem at all if you're reading them by PHP, because PHP obviously needs a HTTP request to be processed and so will receive the cookie as usual, regardless of it's HttpOnly
flag.
The following test case can prove this (open, and refresh):
<?php
echo '<pre>';
var_dump($_COOKIE);
echo '</pre>';
setcookie('TestNonHttpOnly', 'True', time() + 3600, '/', '.example.com', false, false);
setcookie('TestHttpOnly', 'True', time() + 3600, '/', '.example.com', false, true);