I bet they took the games down to artificially create some sort of demand once Returns part 2 hits. I can't imagine the Country series being available for so many years on the VC only for some recently discovered clause in the contracts to have them taken away.
As said above, Jet Pack is the best reason known so far as to why DK 64 was never available.
Rare creations including Diddy Kong, Dixie Kong, Rambi, Squaks, Crunch, Clap Trap(debatable), King K Rool, Cranky Kong, Funky, as well as many Kremlings have showed up in various Nintendo games throughout the GameCube and Wii generations so I doubt there was any contract issue. Granted those are just characters and not full games, I would imagine if it was contract related those rare related characters would go along with it.