How does the engine run at idle? Is it smooth?Those two bolts are for securing the coil pack harness - if they're leaking id recommend checking they're tight and if so they may require a tiny bit of sealant
I reckon someone has drilled through the hole, or a run a screw through it thinking bolts were missing from the coil pack harness, but VW never secured it down from the factory. It just rested over those nubs on the rocker cover.