Maybe my mind's fuzzy because it's late, but are you saying it would make more sense for those who get the basic to not have any way to get Nintendo Land?
Heh, that's the result (except the eShop), but the main point was to just allocate more production to deluxe units to make more of them available for everyone that wants it. If people want Nintendo Land they'll probably go after the deluxe, so instead of printing copies for the basic model owners, go deluxe heavy in production instead. It'd reduce the value illusion of the deluxe without having Nintendo Land sold separately to compare though, like people might think it's a basic cheap pack in of mini games (like how "core" gamers view Wii Sports or something) and ignore it instead. It's a sort of catch 22 situation.
Otherwise I'd guess there's market research and a bunch of financial stuff involved. Printing possibly useless copies of Nintendo Land is probably nothing for them cost wise, but could be worth it as a way of advertising the game itself ("it's a full retail game!") and the more expensive model. If there's not enough stock of a "cheap" model, they could lose out on sales by more price conscious buyers and people that would rather spend the money on a different game (and feel offended by unwanted pack ins increasing the cost for them). There could be a billion random little factors like that involved in the choice.
