When using fill with the replace subcommand, in a superflat generated with the Overworld preset, air isn't present in the patches of water generated on the surface.
It's looks like air but it seems to be a void, as running the fill command to replace the water in the volume will work, but switching the replace filter to air in the same volume will fail with 0 blocks changed. Once the 'void' block has bee updated via a block placement, the destruction of said block will result in air again.

Pre-Commands.png is the generated patch of air and water for the test.
(The white concrete powder block represents the bounds of the volume)

Replaced Water.png is the result of the command shown in the screenshot (as expected).

Replaced Air.png is the result of the command shown in the screenshot.
(Note how it has replaced the air over the lower right white concrete powder block but hasn't updated the main body)

Wool Placed.png shows the manual update pattern to be expected from running the same command again.
(Wool was manually placed and removed before running the command again)

Replace Air (oak_planks).png shows the result of running the same replace air command after the manual update provided by placing and destroying the wool.
(Replaced grass_block with oak_planks to show the change clearer)