Well, all it takes is for e.g. Nintendo to see that you're violating NDA and poof your game is gone from the eShop. So while in practice you can get the API docs, woe to the company that leaked them.
So if e.g. Wesnoth got ported to eShop they'd legally have to publish the source but Nintendo would instantly delist and sue for NDA violation.
Again, I hate the companies that do this. Nobody should buy from them. But that's what they do.
1. In order to publish a game to a console, you do need an agreement with the console manufacturer. (Unless you're doing homebrew but then the point is moot.)
2. In that case, you do get access to the official documentation, everything is solid.
3. The word "legally" has a lot of bearing there. Sure, they have to. And if they don't, what? Will the other contributors sue them? If they aren't willing to do that, then they can get away with it.
4. The context is about someone trying to hack the devices. ("Who knows what some enterprising hacker might be able to glean about the workings of the console by looking at the APIs.") They certainly won't be bothered by NDAs.
The only people who this stops are the people who want to do things "by the book". :P