I have a theory why DK64 is not on VC. Emulation issues might be a problem (if you play the game on emulator, you will see some minor graphical glitches, but the game should be 100% playable and beatable), but there is a second possibility.
DK64 features two more old games inside - original arcade Donkey Kong and Jetpac. With the first one there shouldn't be a problem (Nintendo owns the rights to DK), but Rare owns the rights to the second game, Jetpac. Like Banjo-Kazooie games, Jetpac is available on Xbox Live Arcade (as Jetpac Refuelled - new version with modern graphics, but it's possible to play classic version as well).