It should definitely be cheaper. For some Indy companies, that's why it is cheaper. But not for the stupid reasons you gave.
Anyone that thinks it costs as much to run a server as the complexities of manufacturing physical goods, shipping them around the world, then making room for retailer markup to turn a profit, is a moron.
Add to that, Nintendo isn't the only publisher. But they are the only ones running the show on the server. There are definitely games set
To come out from NIS and Nicalis that will be 10-20$ cheaper on eshop. As it should be.