The cost of the HDD and chassis has a direct correlation to the costs of logistical complications.
Whatever the physical dimentions of the chassis are going to be, you can be sure that it will be manufactured almost entirely out of plastic--maybe a stamping of sheet metal in there as well. Both plastic and sheet metal (think of the metal shield in the top of the xbox case) are extremely cheap to manufacture, especially in China/Asia. Selling a HDD with the chassis, as opposed to without a chassis, isn't going to affect the price of the HDD on any significant level.
What would have a significant impact on the price paid by the end user for the HDD/upgraded HDD etc? Multiple SKU's. This would require different handling of two similar items from the very beginning. Two (or more) distinct packages, two seperate items to be tracked and inventoried, two seperate items to be ordered by distributors/retailers. It would be far less complicated to manufacture one item (HDD with chasis for example) than 2 seperate items (HDD with and with out chassis) and this very well could offset the costs of just packaging all HDD's with the chassis.
Additionally, it's going to be made as simple as possible. Clips break, screws get lost (if you don't have a magnetic screwdriver) and fat fingers jam plugs and bend pins. And that isn't accounting for people who can't/won't read directions.
I could be entirly wrong, but It's my opinion that all HDD (purchased seperately from the xbox360) will be shipped completely enclosed in an xbox360 branded chassis and won't be available as a HDD alone.
That is of course speaking of the available HDD's from MS for the xbox360. As far as adding your own--Let's see what happens when the members of the modding community use their ingenuity!