Hmm, good question. Part of the answer is that drive-thrus are very rare in Japan. But there's at least one MacDonald's in the city where I live that has a drive-thru, but I've never noticed what they do.
Pizza delivery guys will just pull out your change from a coin purse, though.
Edit: Just remembered that sometimes toll collectors on the highways use them, but not 100% of them, so there's that.
I've only been to Tokyo (not smaller cities) but I've never seen a drive-through there. People take the train and walk, not drive.
It reminds me though, in fast food places they often have you order by kiosk and then take your receipt to exchange for the food. So there's no (other) human involved in the transaction.
Fairly common to get some level of hand-contact there when passing around money, credit cards or food bags.