I think they know exactly what they're doing. Selling out in minutes causes news stories, and here we are.
Untrue. The secondary market is currently selling units at a huge markup. I don't think we have a great indication at the moment on how fast the secondary market is moving; it's possible that, whilst Nintendo might have undervalued demand, the resellers are overvaluing it. As others point out, this also helps drive demand to an extent - it's a phenomenon Apple appears to take advantage of from time to time.
They lose nothing monetary.
[1] - https://liliputing.com/2016/11/orange-pi-zero-7-quad-core-de...
[2] - http://www.cnx-software.com/2016/11/08/nintendo-nes-classic-...