No, tornadoes do not affect commercial airplanes flying over or near the tornado zone. Tornadoes are typically too small and localized to have an effect on a large aircraft like a commercial airliner.
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What happens when en route flights encounter thunderstorms? Jet aircraft can safely fly over thunderstorms only if their flight altitude is well above the turbulent cloud tops. The most intense and turbulent storms are often the tallest storms, so en route flights always seek to go around them.
While high winds (a crosswind above 40 mph and a tailwind above 10 mph) can occasionally prevent planes from taking off or landing on time, winds won't put your flight in any danger.
Turbulence might occur during your flight in rainy weather due to the presence of different air masses mixing together and causing disturbances aloft. Warm and cold air masses interacting with each other can result in turbulent conditions high in the sky, making your flight potentially more uncomfortable.
A Cruise ship in port would get damaged and destroyed like any other ship in port when a tsunami hits. At sea: nothing. They will likely not even notice it, as the tsunami wave is very small (a couple of feet) and travels at every high speed (500mph or even more).
The inner pane basically safeguards the load from the passengers during flight. When both the outer and middle panes break, then all the pressurization in the airplane would escape leading to decompression in the passenger cabin. A plane is pressurized for passengers' comfort as it climbs to a higher altitude.
The impact of hitting birds during key sequences like takeoff or landing can damage the engines, windscreen, and nose cone, usually forcing the plane to return. Here's what happens during such an event.