They are available in that quantity. They do make sense up to around that number, although the around 1K is the sweet spot. Laying out and certifying a high speed design (not just a noddy A9 with DDR2) is expensive and it's all NRE cost. The cost of the components for the CM is driven down by the combined volume significantly - if you want to buy 1-10K of those by yourself, you will pay a premium over what RasPi gets them for. You might not need a full 6/8 layer board for the whole product as well. As important, the software support is great as it's just a standard RasPi - you don't have to support your own custom image.