I see this happen to the head bolt pad next to the exhaust but not the other three.
The reason it happens to the one next to the exhaust is because it can get very hot in that location.
The heat can get excessive in that location if you race in a part of the country where the temperature gets hotter that this Yankee can take for very long. Places like Arizona, Southern Ca. New Mexico, Texas and Mexico etc etc.
Other things that can make the engine run very hot are taping off the blower housing, too much header wrap, very sticky tires, and high kart and driver weight and improper ignition timing.
It normally does not affect the other 3 head bolts.
I have seen the flange on the head bolts bend or cup somewhat over time (normally the one next to the exhaust) but i have NEVER seen a head bolt that appears to be cracked or damaged like the ones in you picture. I would like to see a better / closer picture of the flange on those head bolts.
I'm still suspicious of the torque that was applied to those head bolts.
If you bought the engine used the previous owner may have over torqued them. If you are the original owner then i'd still say you better check your torque wrenches.