What would they bundle other than the case? Which I'm sure you'd be able to buy eventually, or if not import
They could bundle a limited edition 3DS with a game. That is all that is needed. I agree that I can't see us getting something like the 10th anniversary box, but Nomura said he was very pleased with the KHDDD announcement at E3 all those years ago and he expressed enthusiasm at the bundle when he was speaking with Iwata. I wouldn't put a bundle too far out of the possibilities.
We might luck out and get a special edition, but like I said the problem with them doing it is low 3DS sales in general and low Dream Drop Distance sales in Japan
Keep in mind not many people have a 3DS, and a KH 3DS might persuade a good number of people to buy one, unlike the PSP and DS, where by the time the games came out, pretty much all the people who were going to get one...had one. Also, Kingdom Hearts always sells more in the US because of its exponentially greater sales as compared to Japan, so I don't think bad sales in Japan should deter them from the other territories.
I've been holding off on a 3DS looking forward to either a KH3D bundle or 3DS slim. Same for a Vita slim/next version, but that's beside the point. I'm looking quite forward to Nintendo's presentation in general. I'm really interested in what they have in store for the Wii-U. Of course, a KH3D trailer is also what I look forward to the most.
A 3DS Slim won't be out by KHDDD's time if that isn't obvious by now, but I'm also curious as to what Nintendo will say about the Wii-U.