IMHO Nintendo does have to take responsibility of their own report. It's not like Greenpeace snuck up on them and used only the information on the website.
Also keep in mind that Greenpeace is an advocacy organization, and giving Nintendo a score of "0/10" instead of a more accurate "N/A" puts public pressure on Nintendo to cooperate with Greenpeace's requests for information in the future.
The methodology of the report means that the score is not about the environmental impact of Nintendo's manufacturing practices per se, but rather the lack of publicly available information about such manufacturing practices.
I think we can agree that greater transparency is a good thing. I think we can also agree that Greenpeace is not acting as an impartial environmental auditor in this case, but mainly as a public advocate.