Big waves can damage a coastal reef when they break, but 100 miles at sea, waves do not affect the sea floor.
As a rough formula, if the wavelength, the distance between successive crests, is less than four times the depth of the ocean at that point, the waves do not affect the bottom.
In other words, with a 1,000-foot wavelength, a fairly big wind-generated wave, 250 feet is where the wave begins to feel the bottom and the bottom begins to feel it.
If a submarine is in water deeper than 250 feet, it would avoid the effects of the turmoil on the surface.
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