Hasn't happened to me but I also grow many smaller plants (30-36 inches tall). Roots do grow down into the bottom. I run an air stone in my res's to ensure as much oxygen as possible is in the water.
Some have gone as far as running a air stone down in the bottom of the outer bucket. thats a lot of airstones, lines and pumps if I were to do that. I think it would be easier to find a way from letting the roots into the bottom pot. perhaps capillary mats or something in the bottom of the inner pots would help.
I have had minimal root intrustion on the buckets....its never a problem. Even when I had that freak plant that was rootbound, I didnt have many toots coming out at all