Dorian,
I'm sure Steve will answer the "bulk discount" question when he gets online and checks the forum, but in the past the answer has always been, "No!" as offering a discount disadvantages the local bricks-and-mortar locations.
As for ships available separately, I don't know. I know their is a limited selection of packaging options available because retailers do not want to deal with an infinite number of SKU codes. You might email Leanna (
sales@starfleetgames.com). She might be able to help you out on single ship purchases.
Or... you could go to Origins this coming year, listen to Jean's speil about "Save A Ship!" and then go through the factory seconds box. I picked up 11 of the large Auxes ($2 each and only needed minor patching) and 4 of the WYN Barracudas (in addition to 38 "other" ships that needed saving...)