This might seem kinda dumb and it most likely is but awhile back I had this idea that the yonko don't have bounties. The WG is always talking about maintaining the 'Three Great Powers' which is the Navy, Yonko, and 7 warlords. So they really wouldn't want that to be upset. As bounties would make people want to take them down they would just get rid of them so there is less incentive.
It may just be because they are so powerful there isn't really a lot of incentive to attack them in the first place so they don't bother with nulling their bounties tho. I just wanted to hear your thoughts on it.