The fan probably has an effect on the ambient temperature in the tank. A slight night-drop won't hurt your snake, but if it's more than several degrees, I'd do something to adjust it. Does your thermometer have a memory function, or can you measure temp while it's cold to see how chilly it's getting?
Possible solutions:
Use the fan at a lower setting
Put the tank where the fan won't affect it
If you're using a UTH you've got belly heat all night. You should be using a thermostat or rheostat anyways. With a thermostat, the temp will adjust automatically to compensate for the coolness of the room. With a rheostat, figure out what you need to set it at to get the right temp overnight and adjust it accordingly when the room temps shift.