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Because its better for business if they buy the other Pokeballs en masse than a bunch of Master Balls that are automatic catches.
Think of this way. If I buy 100 Pokeballs for $10, then I've spent $1000. These 100 Pokeballs do not guarantee me 100 Pokemon, lets say I get 50 Pokemon. So essentially now to get the other 50 I wanted, I would need to at least spend another $500. In this scenario they have made $1500 bare minimum. For the Master Ball, I'd only have to buy 100 of then, I'd catch every single Pokemon and never buy another Ball again. They'd have to charge double for them at bare minimum, for instance 1 Masterball is $20, meaning to catch everything I want it would be $2000. Now while that is a bigger profit, that is all I would have to spend, the possibility of having to spend more on Pokeballs than the $1500 estimate earlier is still there, I could end up spending $2500 to get those 100 Pokemon, now because of that the Masterball has to be even more expensive at $30. This is just comparing the base Pokeball and Masterball, it doesn't equate the pricing difference between Great/Ultra/etc. with Master as well. So in reality, a Masterball would probably be closer to $50-100, which is insane, you'd get better bang for your buck at that point just buying the Pokeball or Greatball.
That mixed with the fact that there is probably some type of special production when it comes to them that isn't easy to replicate on a mass production scale.
