Well Nintendo owns stock in them but they also own a lot of stock in Silicon Knights and we know they don't develop exclusively for Nintendo. From what I know, it is just a partnership. However, I'm pretty sure Nintendo wears the pants in that partnership. Meaning Ninty decides the projects and they fund them. As for creative freedom within that, don't think they try to stop that although knowing Nintendo they definitely have the final say before it goes gold.
Other than that I'm really not sure about anything else. I'm pretty sure though that Ninty doesn't completely own either. I believe HAL is a partnership but due to Iwata's ties with the company, it's a very strong partnership that probably won't be broken. Not to mention Nintendo has already given its head, Sakurai, large funding and his own team to create an exciting project called Project Sora.
