Most external 3.5â€ hard disk enclosures include a small fan. Of all the enclosures for hard disks Iâ€™ve used so far, the fan runs continuously, but can be easily disconnected. The aluminium enclosures will generally work fine with most hard disks with the fan disconnected, especially the low energy hard disks such as Western Digitalâ€™s green power series, as the metal casing acts as a heat-sink. Even with complete external hard disks (such as the Maxtor OneTouch), the fan will generally only operate once the hard disk exceeds a certain temperature.
If you plan placing the external hard disk in an enclosed area, such as on top of the PC under a desk, I would suggest keeping the fan connected. However, if it will be out in the open, you can try running it with the fan disconnected and checking it every 10 minutes during the first day to make sure it does not get hot to the touch.