as far as cutting holes in the hub , and then trying to keep mositure out by using plugs when its wet outside..or avoiding puddles, etc...that wont be good enough. You will still have to deal with the humidity and mositure in the air during the summer months ,which will build up in the hub motor.
I would think, if you are going to drill holes in the side covers, it would be mandatory to use the CRC Red Urethane Seal Coating to provide moisture protection of all internal components....not doing this, would probably result in the motor failing as it builds up moisture inside and causes problems.
I wonder if it is really needed to drill so many large holes in both sides of the cover. I would think the air cooling could work fine, by just drilling 1 hole on the freewheel side near the outer hub area , about 1-2 inchs wide at the 12 o clock area and then place a 90 degree elbow in that hole, so it fits snugly in the hole and epoxy it in permanently so it faces towards the front of the bike , then drill another hole of the same size at the 6 oclock position ...as the wheel turns, air would be forced in the hub at the elbow hole and forced out at the normal hole .