There are some cargo aircraft that have windows which are not covered. Look:
On the second deck above where it says "Hong Kong Asia's World City" the aircraft has 3 uncovered windows. Source: Airliners.net
Also here:
Source: Airliners.net
On the upper deck of the Martinair 747 the windows are not covered. My question is: if the aircraft is used for cargo, why do they leave the windows uncovered?