The code is explicit in not taking care on that issue.
Not wondering why, I see no reason not to update discount uses when an order is deleted.
in uc_discounts.module, funciton uc_discounts_order() , change

    case 'delete':
      // Delete existing order codes
      uc_discounts_order_codes_delete($arg1->order_id);
      //TO DO: determine if uses should be deleted or put global setting in for user to decide
      break;

with

    case 'delete':
      // Delete existing order codes
      uc_discounts_order_codes_delete($arg1->order_id);
     // Delete existing uses of codes for this order
      uc_discounts_uses_delete_for_order($arg1->order_id);
      break;

This avoid manually updating a database every time an order is deleted (for testing purpose for example)