I don't know that particular Yamaha, but in the past I've removed the drive parts and filled the hole with JB Weld. There are block off plates for some models. Currently I've left it on my 360 Enduro. It's a street legal dirt bike and the convenience of getting gas at a gas station means I can go hundreds of miles on one tank of oil vs 60-70 on a tank of gas.
No need to do anything about the carb. It won't care, but you should also block off wherever the oil gets fed into the intake. Usually that's downstream from the carb but you will need to find it and close it off to prevent an intake leak.