Input format to save page links by ID but render by the URL alias?
If you use an wysiwyg editor ie. CKeditor, there are contrib modules that offer you this functionality. For example, take a look at the ckeditor link module.
It let's you search for your nodes and make a link to the node path which is what is saved to your database. Drupal automatically shows the url alias frontend, so if you change your url alias at a later point, you will still have a working reference to your node.

Why is it important to you that you reference them by their current url alias?