Why is there a 1/2-inch hole drilled in my heater exhaust?
The short answer is this: it makes no sense for a sealed combustion appliance to intentionally leak exhaust gases to the building interior. There was probably a legitimate reason for the hole to be drilled -- maybe there was a need to measure the pressure inside that pipe to assure the installation was okay, or as part of the troubleshooting of a "blocked exhaust" error code thrown by the furnace controls -- it's difficult to be sure. In any case it seems reasonable to seal the hole.

I can't speak for your specific appliance, but in general, yes it's normal to have condensate when longer exhaust lengths are involved. The liquid may flow to the exterior or back to the appliance depending on the slope of the exhaust. Some appliances are designed to receive and drain the condensate; others are not (but a condensate catchment accessory may be available). Consult the appliance installation instructions for details.

You mentioned both an air conditioner drain and a heater drain. Does the heater drain originate in the inducer fan housing? If so it sounds like your furnace is equipped to deal with condensate. I'd verify that the drain is working, maybe by running a few ounces of water in through that exhaust hole and verifying that most of it flows out the drain. Then seal up the hole in the exhaust pipe.

Exhaust condensate is somewhat corrosive (acidic), so it should be handled with materials designed to deal with it. A puddle of condensate on the floor is Less Ideal.