Nintendo probably didn't ship very many copies if it's being sold out at places. Nintendo does this sometimes, even with popular titles. They lack any type of confidence in some things and that stunts the game's sales.

However, I have a feeling this is a limited case.

Our local chicagoland GameStop, near where I live, had ordered fifteen copies when I asked on picking up my pre-order. All but one, used as a display unit, has been for pre-orders. They had all the other pre-ordered copies hidden behind the counter.

Don't think they order much extra for anything that isn't "Mario".

Nintendo (and any other publisher) ships what retailers order. There is no "undership", there is undervalued demand based on pre-order numbers as that is what retailers use to judge how much to order. In this case, it seems that either the retailer didn't order any of the title or significantly undervalued the demand outside of preorders... which is understandable as its: a niche game, sequel to a poor seller, and a WiiU game.

My pre-ordered copy was hidden behind the counter, but on the actual shelves they had 3 copies of the game when I got there a few minutes after the store opened.

That would make perfect sense for Bayonetta as it is very niche, but under-stocked games have happened several times before for other fairly popular Nintendo titles. Either retailers aren't ordering enough for whatever reason or Nintendo didn't make enough to meet demand on the first shipment. It could be both.

Went out to the shops today. Walmart and Target were sold out. 1 copy left at the gamestop but I didn't think to ask how many were sold. Tried some of the smaller shops and no luck there. I wouldn't have thought they even stocked them if I didn't see a slot for it there.

I'm afraid that Nintendo of America (I'm not sure about Europe, but NoE are generally a lot better than NoA) are using core-oriented titles for a rather cruel experiment. They're supply constraining these games while promoting them on eShop to see how many of the core market can be pressured into "buying" digitally.

I believe they made this quite obvious with the FE Awakening launch (I'm trying to remember the thing that suggested this... probably a leak), and the fact that this is a continuing trend with these titles makes me consider that it's an ongoing project.

We faced a similar issue here, the distributers for our region ordered very few copies, then after the demo and the reviews there was an increase on pre-orders, but it was too close to launch, so Nintendo took another order but is not going to be available for us till at least a week. The orders were placed but the timing is what is making the game unavailable in some places. The sellers understimated the game a bit and after they made the adjustment it was too late to correct for the first batch of copies, a second one should be available very soon.

Reckon this will hurt sales,  or will people who missed out simply pick it up second or third week?

From what I have seen in my country (very tiny small market), people will wait up to 2 weeks, after that used copies will start appearing and players will start focusing on Smash, it can be worse in other countries with a more stablished used market (handled by the same game stores), but at least people will wait a few days till the next store visit (usually done on tuesday for new releases in USA).

The thing is that the game is not sold out everywhere, just that some stores (maybe the one closest) will not have it and if you really want the game you can always find it or order it from a big online store like amazon. The effect on sales should not be big, maybe a 5% decrease from spectations of the first week, nothing more.