Aviation’s question answered:
Those windows are called eyebrow windows, and they were designed on many aircraft, not just Boeing.
The purpose of the eyebrow windows (1960’s-1990’s) was to allow better visibility in turns.
They were also used to help celestial navigation (navigating by stars) before the advent of today’s computers and avionics.
Another part of the celestial navigation equipment included a viewing hole in the ceiling of the cockpit for the navigator, such as on the DC-8 aircraft.
Today’s aircraft have sophisticated equipment on board, such as anti-collision systems. Visibility during turns has become less important, although “see and avoid” other aircraft always is still a golden rule.
By eliminating eyebrow windows additional fuel savings and a quieter cockpit are also achieved.
Making the cockpit quieter was truly welcomed by B737 pilots, one of the noisiest cockpits around, even today. This partly because even new B737s are still based on much of the original 1960’s technology.