I'd like to hear a logical reason as to why Nintendo would deliberately do this.
Well, to be fair, Nintendo does have a long history of manipulating the market. They did a LOT of dodgey stuff in the 1980s that left a sour taste in the mouths of consumers and got them in hot water with various governments. They've undersupplied retailers all the way back to the NES, both with consoles and with games. At this point, it's pretty much expected.
Personally, I think it means that Nintendo cares more about their bottom line than anything else. They'd rather a supply deficit than to have an over-supply on the books for the year.