Year to year comparison...........no real differences in cooling.
I prefer the short pump, as do many others. They give you room to run a mechanical belt driven fan in the cars I build (early Fords with Chevrolet power)
There is also a lot more after-market support for the short pumps (pulleys, brackets and after market water pumps).
There is another pump available that a lot of 32 Ford people use (myself included)........the Zip raised water pump. It is a aluminum housing that a 6 cylinder Chevrolet pump fit into. The fan centerline is raised 5 and 1/2 inches. Then you use short water pump pulleys. The Zip has the alternator bracket cast into the housing.
I have one on all the 32's.
I use a Edlebrock aluminum water pump on the 40.
As you can see.......I have to space the fan out almost 1 inch to get the 16" fan up close to the radiator.