exclude pages in custom menu

You probably want to explode your list of page ID’s using the explode function.

Something like;

<?php
    $exmenuitems = explode(",",get_option('exmenuitems'));
    $recentPosts = new WP_Query();
    $recentPosts->query (array (
    'post__not_in' => $exmenuitems,
    'post_type' => 'page',
    'showposts' => $menuitems
));

I’d recommend using the WordPress Menu building functions and admin interface. Its much more intuitive for end users to build their navigation menus via drag n drop that using page ID’s.