I have two examples of buildings not flooding when covered by polluted water.
the kiln keeps right on working as does the air deodorizer. in fact the latter pushes the water aside creating a very nice ripple effect.
edit: Flooding does occur as normal on when you load a save.
build yourself a kiln and a deodorizer building. Then have them get flooded with up to a full tile of polluted water and watch them keep working. Building one in a tile already full of polluted water gets flooded as expected. Flooding does happen when you load the save.