Im resonably certain from reading about chainless bicycles that you only loose about 5% to the chain. granted, the chain will wear out much faster then it normaly would because you are applying so much power to it. There is also the aspect of constantly having to maintain your chain and oil/clean it.
In short, im pretty sure that chain driven is always as efficiant or more efficiant then a gearless hub motor, but it carries with it much more maintainance. I think lowell at one point said he was swaping chains out every 1000 miles. Im not sure how much you will be riding but for me thats something like every two months.