As long as you don't have a OCXO timebase, which I highly recommend you looking into, the fan is not going to do much. It is supposed to keep the inside of the case at a constant temperature. But with only the TCXO timebase, there isn't any cooling necessary when the counter is off.
With an OCXO, however, because it is always on to provide the highest possible stability, the fan would be constantly on as well. So get something silent.
Getting a decent reference oscillator is pretty much mandatory for this counter. It is such a fine, precise instrument, but the built-in TCXO is rubbish.