He was actually silhouetted out in the DKC and DKC2 manuals. I remember them both. And I don't think they mentioned him by name.
In DKC2 he's mentioned IN-GAME. You have to go into the very first room of Pirate Panic (first level of the game), similar to the ability to walk into the Banana Hoard and DK's hut in DKC1. Kaptain K. Rool is namedropped in a note you can find in there where he explains the plot of the story; he kidnapped DK and will only give him up in exchange for the banana hoard.
Interesting. Very interesting.
I don't think it means much personally. There's two explanations:
1.) Nintendo contacted Microsoft to secure the licensing to ensure it could be on VC unalterred.
2.) We were completely and totally 100% wrong, Nintendo didn't have to do anything with Microsoft, it wasn't released before due to technically difficulties getting it on Wii or they didn't think it was popular enough and didn't bother releasing it (more likely technically difficulties).
Frankly, I think its just #2. Nintendo published the game, they own all the publishing rights. Microsoft had to go through Nintendo to get Banjo-Kazooie on X-Box because Nintendo owned the publishing rights, but Nintendo did not have to do the same in this case.