Do you want to put a coil tap or such like on the pickup, or just leave it as standard? They refer to the wire from the pickup itself to the pots.
If you think you're going to want to add a coil tap at a later date even, go for the 4 conductor wiring.
If you're happy with the standard humbucker, and that's all you're after, then go with 2 conductor.
FWIW, I'd get the 4 conductor wiring, just in case you want add something to your tonal arsenal sometime later...