I was thinking the same thing as VGrevolution. They could always add "rumble" later, whether it be an overall emulation tweak or asking you to re-download the game.
However, if the Classic Controller doesn't have the hardware to give you force feedback, which I believe is the case, you're only going to feel it if you can use GameCube controllers for N64 games. And not the WaveBird, but wired ones, and seeing as how I've cleaned up my room for maximum playing space with the Wii next to the TV, wired GCN controllers are out of the question anyway.
Because of the inconsistencies between the original Nintendo 64 controller and both the Classic Controller and GameCube controller (I'm looking at you, C-buttons...and no, C-stick doesn't cut it, for the umpteenth time...and position of Z...etc.) I'm thinking that most N64 games will actually have to be tweaked regardless (instead of straight-up emulation of an exact copy of the original code).