I have created a custom post type and disabled it from appearing in search results. However when I add a link from a normal post, I still get these entries from my custom post type available to link to in the internal linking box (at the bottom when of the popup when you click the link button in the editor). How can I disable the custom post type from displaying entries there as well?
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I suggest making it private ('public' => false when registering the post type). You could club it with 'show_ui' => true to still display the admin interface.
See the codex for register_post_type for full reference http://codex.wordpress.org/Function_Reference/register_post_type