You should have a set fee to set up a basic eCommerce site. Then you should have a set fee for adding products over and above your basic setup fee.

The way I go about determining prices is I contact the service providers and give them a scenario I would like them to quote on. I have been quoted $12,000+ for setting up large eCommerce stores (up to 300 products), then $20/product over that. This was the lowest quote I received. Two of the providers explained their reasonings, saying that an eCommerce store is just as, if not more, important than a bricks and mortar site. An eCommerce site carries almost none of the overheads a bricks and mortar store carries and can earn you vast amounts of revenue if marketed right. eCommerce stores are also infinitly scalable etc. That was how they justified their prices.