You can create a Custom Field radio button called hide_from_menus with values yes or no t then use Query posts by custom fields.
Then in your query, add meta_key and meta_value. Example:
$args=array(
'post_type' => custom-post-type,
'post_status' => 'publish',
'posts_per_page' => -1,
'meta_key' => 'hide_from_menus',
'meta_value' => 'yes'
);
Be sure though that you update all your posts (re-publish) so that it will have the key value that you specified.