That's a valid concern, but what does a non-disclosure agreement have to do with that? If they don't want people to use their API, can't they just not authorize them to use the API? I don't see how a full NDA is necessary for that.
Maybe so the initial impressions of an incomplete API won't make others think that it isn't a platform worth developing for? I really don't know the answer, but I could see it from a "brand image" perspective. You don't want people spouting all over the internet how much v0.0.01-alpha of your API is absolutely terrible and turning other developers off to your platform in the future.