When I use a water bucket it often happens that the water disappears like you would expect, but then doesn't get 'filled up' again by surrounding water or flowing from surrounding water (tested in open waters and self made pools)

It does happen a lot more often on the water surface but it happens underwater too.

Even though the waterblock is not rendered, if you go underwater and in that particular waterblock, you will still lose your breath, so it can't be exploited for airpockets underwater.