Presumably they just charge what they think people will pay. I've noticed that Dell (here in Australia at least) do a similar thing. They have a reasonable price for the base machine, but charge far more for any upgrades (RAM, hard disks, etc.) than the components would cost to buy retail.
If you need a lot of storage you might want to consider building yourself a simple headless (no monitor) Linux box. It would give you the option to add more hard drives as you need them, and as the prices inevitaby come down. It would of course require more work to set up, but once it's set up it should require little or no maintenence.