the outside of the motor will always be cooler, than the windings, so the ir thermometer IMO is not going to be 100% accurate.
commenting about the direction of the fins
If the fins were placed elongated around the motor there would be much less surface area to "cool" by placing the fins across the motor there is a ton more surface area for the air to hit.
While that makes a lot of sense, it doesn't explain why there is a 20 degree F description between the motor temperature and the air temperature after the bike has been sitting in the garage for a day or more.
However, you could argue that what difference does the temperature reading make? All you really have to know is at what temperature on the gauge does the controller start cutting back on the power on your particular Zero. After all, the temperature gauge is not supposed to be measuring the ambient air temperature, just the temperature inside the motor.
In any case, for me, overheating isn't an issue as I use my Zero just for transportation, not for sport riding. For that, I will use one of my IC motorcycles as they all handle and ride much better than my Zero (thank you Fast Ace) and I prefer going around tight curves to going fast in a straight line.