After having explored an area of about 1000x1000 within 5<y<115, I can comfortably say that literally every cave or mine shaft has been flooded, not a single one has not been, with the exception of rifts/canyons.
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Comments 4
After some looking around I realized that this was in an ocean biome. Giving consideration to this, however, doesn't make it any more logical that every single cave within 5<y<20 would all be flooded where there is a floor of approximately y=60. Some makes sense, but definitely not every single one.
Duplicate of MCPE-125379.
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This also happens on Windows 10.