I do not know why Atari falcon designers put a fan there. May be to cool the all box of the falcon or maybe for an extension that never came out.
I just want to tell you a little story.
Many years ago, my brother was seeking for a fan to put on a ST machine ! why ?
Because the summer before he had to make his st repaired. The glue did break because of the heat and the plastic of the box started to melt... The st did work many many hours long without any pause in a room at about 28 Celcius degres. The summer was hot and the st's glue didn't cope with.
So remove your fan if you want but don't be surprised you reduced the expected time of life of your machine...
At least, be careful about the temperature of the room the machine is placed in !