Aircraft fuselages are not balloons, and they do not catastrophically pop if the fuselage is punctured in discrete locations. Relevant recommended viewing is "operation guillotine fuselage test" on YouTube, where large steel blades are dropped through pressurized aircraft fuselage sections to validate no explosive decompression. In the late 1950s, BTW.

Commercial aircraft are required to be designed to maintain 15,000 foot equivalent cabin altitude after any probable failure, which includes multiple missing windows, per the requirements of 14 CFR 25.841 and it's EASA equivalent.

There is already regulation in place that should have caught this but did not. The captain is required to perform an external visual inspection of the aircraft before departure, which follows a checklist that includes looking at the windows. It appears that did not happen.