GP40s and GP40-2s were turbocharged locomotives. Therefore, they had only a single exhaust outlet on the roof, from the exhaust side of the turbo. Same for the SD40 and SD40-2. The turbocharging was how EMD got 3,000 horsepower out of that 645 prime mover.
Non-turbocharged, second generation EMD power (the GP38, for example), had two exhausts. Some older, non-turbo’d EMDs had four.