I had to solve this same problem for Ubercart 3.0-rc3 (Drupal 7).

After many failed attempts involving a module with hook_uc_invoice_templates and hook_theme_registry_alter, the solution that finally worked for us was to make a copy of both uc_order--customer.tpl.php and uc_order--admin.tpl.php and drop down to my default theme's root folder. Please note that both files uses two dashes. Just for reference, both files can be taken from /ubercart/uc_order/templates.

You should then do a hard clear cache to make sure changes applies (I recommend to use "drush cc all", twice for better results).