You do not take into account the status of the fans, when you perform a short circuit calculation. If all else is held equal, the fans will have no affect at all on the fault current supplied by the transformer.
A transformer?s KVA rating is based on its ability to reject heat to its environment. Adding fans to a transformer design will increase its ability to reject heat. Since a wire?s resistance will vary with temperature, running a fan will change the winding resistance, and thus will change the fault current available. But that would not be ?holding all else equal.?
So put it this way. Run the transformer with fans off, and load it to some high percent. Measure the winding temperature. Under those conditions, the transformer will have a particular value of resistance, and would supply a particular amount of current to a fault. Now turn on the fans, and load the transformer until you get to the same winding temperature. This will require you to add more load than before. But under the same conditions of winding temperature, the transformer will have the same value of resistance, and would supply the same amount of current to a fault.