While not useful in all cases, one should never miss the opportunity to take the coward's way out when possible. When modeling warships, consider modeling the ship at General Quarters. In such a circumstance the window would probably not be visible as such. WWII USN warships would have an airport / porthole unit that looked like this:
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When GQ is set, the glass panel is hinged inward and a metal plate ("deadlight") swings outward to seal the hole from water and splinters. The outer surface of the metal plate is painted the same color as the ship's exterior / camo. In other words, no special painting is required.
You would not want to drill out the airport / porthole since the outer surface of the plate would be flush with the hull outer shell plating. I have used P/E portholes applied flush to the hull with no hole, then painted the hull. You could lightly highlight the round airport / porthole frame if you wish.