David Doak and others left long before that to found Free Radical. Nintendo sold Microsoft nothing more than a shell and some IP's they had no interest in anymore. Which is why the price MS paid was so laughable.

But M$ owns the rights of all Rare games, DKC included?

No they only own Rare developed IP's. Starfox Adventures and Donkey Kong Country were developed under licence from Nintendo.
Rare own Perfect Dark, Killer Instinct, Conker, Jet Force Gemini and Banjo Kazooie.

Then you may as well also throw in a mention of Commodore. Again, completely different company, but the logo is still going strong.

I personally don't care what a developer's logo looks like as long as the developer makes a good game.
Also, I wouldn't say that Rare has really gone down hill since joining Microsoft considering the fact that they made Kameo which is a great game. I finished it not too long ago and it's a fun and pretty charming game.