The original Boeing 747–100 had only 3 windows on the upper deck. This was back when airlines were using the space for lounges, so the three windows provides a more comfortable atmosphere.
The original three window upper deck.
Later on airlines decided that they wanted to put paying passengers on the upper deck, so having only three windows doesn’t make sense. Boeing decided to have 10 upper deck windows as standard instead of just three. They also offer retrofits for airlines that already have the original windows.
An example of a retrofitted window. You can tell from the different patina on the window portion of the upper deck fuselage, compared to its surroundings.
Some airlines however decided that they rather like the three window arrangement. Since the 10 window arrangement is now standard, Boeing just offered to plug the 7 windows so from afar it looks as if there’s only three windows on the upper deck.
Both pictures above are of the same aircraft, N93119, which blew up after take off in 1996 as TWA 800. You can see that from afar it looks to be a normal 3 windowed 747, but upon closer inspection you would be able to see the plugs covering the excess windows.