If you look at the Boeing 747-8 – the final 747 variant which has freight (no windows) and passenger (windows) versions which were developed simultaneously, the “overall empty weight” is about 220 tons for the passenger version and around 197 tons for the freight version. This is a weight difference of just over 10% and I would imagine (though cannot be sure) that a large proportion of this difference would be accounted for in seating, locker space and galley equipment. It is true that the freight version has thicker (and hence heavier) wings and larger fuel tanks. It could be, of course, that the fuselage structure of both is similar in design (to avoid having to design two different versions). But I have always understood that the principle mass of reinforcement required in passenger aircraft stems from the strengthening needed to cope with cabin pressurisation (common to both the passenger and freight versions).
I would be very surprised if the structure needed to facilitate windows in a pressurised aircraft accounted for 50% of its weight.