When talking of third-party games, I'm inclined to say that Nintendo is using shipped numbers, especially since they know which companies have asked them for more than a million discs. I don't know that they internally track sales of third party titles.
However, when talking about first-party games, you could speculate that Nintendo posts their own internal sell-through data.
Regardless though, I think the error in these cases is less so than that with HD consoles. Publishers who talk about games on other systems often completely front-load their shipments, which can yield a huge disparity between what they say and what NPD data says (see: Ubisoft announcing early on that 2.2 million units of the latest PoP game shipped, while December NPD suggests that just under 500k sold in the US). The Wii I suspect is, ironically, less susceptible to this kind of over-reaching PR since I doubt most Wii games start out with shipments more than a million. Most Wii games I suspect get restocked to go over a million as demand continues over time.
In hardware, Nintendo usually sticks to shipped-to-retailer numbers I believe. The reason Sony got in trouble with this terminology was that they were using shipped to Sony warehouses as the definition.