Here is what happened most probably:
Nintendo has people that go around defending their IP's on several supports. The request of EVO got thrown in with the request from average joe's site. The standard Nintendo reply by their lower ranking worker is no refuse these requests in a polite form.
EVO goes public saying they got this response. Fans are displeased and this reaches the ears of higher ranking workers on the company. They immediatly order the mistake to be rectified since its not average joe's site but a show with lots of exposure.
Thats basically what happened here. The low ranking worker has no clue who these sites/organisations are and the higher one does and had to rectify the decision.
Is Nintendo clueless? No, otherwise they wouldnt have reverted the decision so fast.
Is the lower ranking worker someone who doesnt know or care about videogames? Probably yes.







