It's because people will pay $80.
This is a common misconception, that the price of a product is calculated using "how much it costs to manufacture, plus some profit margin percentage". That is false. Cost to produce only sets a floor on retail price (and sometimes not even that); apart from that they have nothing to do with each other. You charge what the market will bear.
I believe Nintendo would be better off making little to no money on the Joycons. As a spillover of Switch owners having more Joycons and thus the ability to play with their friends, Nintendo will sell more multiplayer games and more Switches.
The drawbacks are the missing motion, "minus", and ZL buttons. If the game works without that and you have some gamecube controllers already, getting an adapter could be a good idea.
What's funny if you abstract this concept out a bit in becomes "I believe the company would be better off making little to no money on their products."
Joking aside, that sounds like quite the gamble to me. And it doesn't appear to me that Nintendo likes that gamble, as they have been pretty averse to taking losses on hardware in the past.
Not to mention I don't know of too many other console makers that are willing to take losses on the accessories.