When I was just a lad studying the black art of engineering, I asked the same question.
The answer was: If the thermostat is horizontal, it makes no difference, but if the thermostat is vertical the hole must be at the top.
The reason, apparently, is to allow any air that is in the system an escape.
This ensures that the business end of the thermostat is fully immersed in coolant.
I have always used this rule and never had a problem.
Hope this helps
