The load carrying capabilities of the fuselage with a larger window will be reduced, but maybe not as much as you might think. If the width of the window remains the same while the length is increased, the load capabilities in the hoop direction will remain essentially the same. There will only be a decrease in the load carrying capabilities in the longitudinal direction. Depending on the original load capabilities vs actual applied operating load, there could be a reduction in the maximum operating differential pressure (causing a reduction in the operating ceiling). If the actual operating loads are less than the ultimate load capability by a large enough margin, you might not have to reduce the ceiling at all.
To the reason of why you don't see large windows often, the major factor is cost. From the design standpoint, it would be easy to design larger windows into a new aircraft. Unfortunately, larger windows cost significantly more money, and the cost does not increase in a linear relationship to the size. Most operators don't want to shell out the extra money for a "luxury item".
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