It's a weird balance. Nintendo makes most of their money on software. Turning a profit on hardware and peripherals is extra. If they lowered the price, they may sell more, like how you might buy 2 of something if a second is half price instead of just buying the 1. However, Nintendo probably figures (or flat-out knows), they will make more by just marking up hardware and peripherals since people have to buy these things (and most likely will) to get the most out of their products.
I will probably end up getting 2 Pro Controllers. Looks like it's back to man-whoring so I can afford everything...