It depends how you want to do it.
For example, you could do that:
You set a quantity greater than what you really have, 20 more than what you have.
Then, in the file "cart" of the view "checkout" that you can edit via the menu Display->Views, you can add the code:
if($row->cart_product_quantity<20){
$app =& Jfactory::getApplication();
$app->enqueueMessage('item '.$row->product_name.' is on back-order and therefore might take longer');
}
after the line:
if($group && $row->cart_product_option_parent_id) continue;