Bryan and Steve are probably along the right track.
If it is possibly for crankcase ventilation/vacuum.... and the hole was for a piece of hose/tubing from the valve cover to the air cleaner base, then it would be similar to a PCV set up...
The EGR would need exhaust gasses..thus would take a tube from the muffler (since there is no crossover ports on a 1cyl Kohler like there is on a vehicle)to the airfilter base plate.