That 'hole' is just a receptacle for a 'cable retainer.' I've included one of your pics, and a picture of that same area from my bike (note the aftermarket cable retainer).
The hole does not go all the way through the crankcase and in no way contributes to water getting inside the engine. The presence of oil there is curious, but could not possibly come from that so-called, "hole." I'm thinking the oil may be a bit of chain oil seepage from the front sprocket cover.
I'm not sure why the sight glass is completely covered... maybe the angle the bike is sitting at, or possibly the crankcase was overfilled. But I can assure you, that "hole" you pointed out is NOT the culprit of anything.
