Yeah, limiting the orders makes no sense. It feeds into scalping but Nintendo gets no additional cut from that, only the original purchase price, so there is no benefit for them to encourage it.
Maybe they figure having a limited edition will encourage day one sales but then it should still be an open pre-order. Personally I have enough of a backlog that I'm not going to get this game day one, but I am interested in it. A special edition could in theory encourage me to pre-order but only if I can ensure a copy and it's an easy process. I'm not even going to try because of how things have gone before and if I did try and didn't get it that wouldn't necessarily mean I would buy the regular version on release day. I would probably go back to it being a purchase at a later date. But a special edition that's easy to obtain might rope me in. That strategy has worked in the past.