That's an inherent weakness of the hook system. Any two modules that define hooks could have a namespace collision. It happened when we added the workflow-ng requirement because it had a hook_configuration() in it. uc_store_configuration() was a menu page, so it had to be renamed. Which isn't really that big a deal, once you know to look for it.

I don't worry about having a collision over hook_order(). "Order" by itself almost needs some clarification to be useful, unless you're already talking about an ecommerce application. You can't use the e-commerce module along with Übercart anyway, so that isn't a big deal.