A couple of points come to mind in response to your suggestion:
1. If the paperwork for a lorry arriving at a port in the Republic shows that it's destination is a warehouse in Dublin, there will be no duty to pay. If the paperwork shows that its destination is a warehouse in Belfast, there will be duty to pay. What's to stop an importer from declaring that the destination is Dublin when (either directly or with a stop in Dublin on the way to add an element of truth to the declaration) it's actually going to Belfast?
2. If a manufacturer in Dublin wants to send goods to the a buyer's warehouse in Belfast, there will be duty to be paid. (The same will apply if it's a Belfast manufacturer sending good to Dublin). So where will those consignments come to the attention of the relevant customs officials?