Yeah, Man, for the health of the stuff in the nute soup. I never agitated until I used organic nutes, and found out it was recommended for the critters. I don't use those nutes anymore, but do use organic supplements, so I still aerate each res.
I don't know about changes in the O2 levels, but I do know that the air is mixed at the surface, and all an airstone does is roil the surface. So I just run a water pump in the res that moves the surface.
Ohhh, in the bed with the plants that fills up! I gotcha, but it's not necessary. What you want to do is have the airstone in the rez, and running 24/7. That will keep the soup oxygenated, and any critters living in it will be happy. When you flood the bed, it will be with well-oxygenated soup.