GameStop employee here, going to do my best to explain what's happening.
When a company has something like a product, a place like GameStop will buy X amount from them. "Hey Nintendo, we're going to want about X bundles from you guys." Other times, Nintendo will be the ones setting the amount, "Hello GameStop. We're going to make X bundles, and you can have Y of them."
Now, this limit is sometimes known from the start, others it isn't. Depends how limited a run the item might be. A standard copy of the game won't have a limit till very close to release. GameStop will preorder as many as they can, because the producer will have lots of copies regardless (Call of Duty, Pokemon, etc).
Collectors editions and special bundles are of a more limited supply. GameStop watched the numbers, and put a halt to it when it hit too many. The company won't be sold out completely probably, it'll hold onto some extra to help with customer issues, to sell them as extra in locations that have a good shot at it... or a number of other reasons.
I can't speak for other retailers, but this is likely how it'll be there as well. A limited product like this typically has a limit of course. X people preordered, that's all X of the bundles.
Now, not all hope is lost. Some people might cancel their preorder last second. It's a tough window... but if someone cancels after the shipments, a store might have an extra copy. If they cancel too far before the launch, chances are your local store won't see that copy, and it'll instead get shipped elsewhere. They might also cancel at time of pick up, or there are going to be people who forget to pick up their bundles as well (usually a GameStop holds a product for 48 hours after release, but some stores might hold onto it for longer, like my store likes to do).
Another potential solution GameStop I know has is something known as "Web in Store". Essentially it's like making an online order, but while in the store. This particular service has its own stock (that I think is just linked with the website's stock). Sometimes with rarer items, we'll have extra ones there. Can't find a thing in store, perhaps we can order it for you type of deal. Free shipping can take a week, and I don't know how upcoming stuff will work with that. I personally am not sure if we have the bundle available on that service as of right now. Sort of like the Zelda Monopoly sets, it's something that'll just come and go as quantities change.
Of course things like Amazon will have a chance to have stuff change on the fly as well.
If you're desperate for one, don't be afraid to politely talk to your local stores. See if they know if they'll be getting extras (not a lot of places do it, but some stores will do fake preorders on rarer stuff to make sure they get an extra or two), if your name can maybe be added to a list, or if they have some web in store type options (I'll try to remember to check Thursday when I work).
Now, with all this said, I don't know how lucky you can get. Where I work, we're out of 3DS copies of the games with none on the way in the next two days at least by the looks of it. This happens to be the for a standard version of the game on the better selling console. If you're not sure you can get the bundle, make sure you preorder the standard game and any extra accessories you might need. A preorder is never final. If you preorder the stuff separate, but you get lucky and your store has an extra bundle, you can get your money back on those extra accessories and such. What you put down is always your money after all. The worst that'll happen is that said employee you're working with as you cancel them will have a bit of a lower performance number, but the cooler employees will totally understand why and not be mad about it.
I don't just have a bad feeling about how many extra copies the standard game will have, I have a feeling that both adapters and controllers will be rare at first. If Nintendo is failing to meet demand for the 3DS version of the game, I can't imagine they're going to ship out a bunch of the controllers. I know it sounds like I'm trying to sell for GameStop, and I'm really not. Go to Best Buy for all I care (well, they're preorder system isn't the best from what I hear, but I can't speak from personal experience). The point is, if there is something you want, something that's niche like the controllers, it won't hurt to secure you get one.
One final word... holiday times can be rough. One year when we had collector Zelda bundles (the one with the sweet gold remotes) our bosses were down our throats to sell them. Didn't matter what sob story the customer had, we were to sell them after at 48 hours (I think some stores caved and sold sooner than that). Sadly the hands get tied at times, and we can't do crap about it. If you have a fancy bundle, try your best to get there that first day (I'm sure most on this site are hyped enough to make that happen). It doesn't happen often, but one holiday a few years back it did, and I just want to be fair and upfront with you guys.
Wow! Sorry I've rambled this much! Just wanted some tips and such out there for you all. Best of luck to those who didn't get the prorder of the bundle, hopefully you'll get all your Smash wants and needs this holiday. November 21st can't come soon enough!
(P.S. Amiibo's can preordered too. So those who are collectors and don't want to risk losing their chance to get a sweet figure because some mom thought it would be cute for their kid, perhaps consider dropping 5 on one of those as well (or in my pathetic case, like 8 or so since I'm getting a double or two probably as well).)
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