Why weren’t the Comet’s overhead ADF windows roundified along with its passenger windows?
It wasn't the square-ish windows (they still had round corners, just not as rounded as modern square windows).  They knew square windows were less than ideal stress wise and built the frame structure to take the expected loads.  They just screwed up the calcs and didn't quite make them heavy enough.  

The problem was stress concentrations at the rivet holes in the areas of the corners were higher than calculated.  They could have just beefed up the structure with more rivets and doublers.  The switch to round was to alleviate the stress problems without the weight penalty of reinforcing the structure.

The holes in the roof were already sufficiently beefy, or perhaps they added a reinforcement.  You will see square holes in pressure hulls on various airplanes for component pass-through all the time, where a square hole is desirable for some reason.  If you make the frame heavy enough, it's not an issue.  It's just that a round hole is a bit lighter than a square one so most of the time a round hole is preferred.