This topic has been brought up a number of times before and in one case actually solved by adding a multiplexing circuit using passives, but I thought I would add to the possible search results for anyone looking at this problem. (The problem being that both nunchucks would have the same I2C address, so it’s an issue you might have even if you’re looking at some other I2C device)
There are chips that look pretty easy to use (disclaimer: I’ve not actually used one yet) that provide multiple switchable I2C channels. One example is PCA9543A which provides two channels. It’s about £1.30 at one off (although I haven’t seen a through hole version yet) and the datasheet makes it look pretty straightforward.
Essentially, you’d be sending and receiving I2C messages to/from the chip which would relay to either one nunchuck or the other depending on the level of a switch line (I think).
I might get one and try it out as I recently got a couple of the wiichuck breakout boards and I quite fancy using two nunchucks to produce MIDI.
If I have a go and find anything contradicts the above, I’ll post back.