The beneficial bacteria(BB) will get it's oxygen from the water. In a wet/dry setup the scrubbies work well because the can expose a large area with a film of water on it to oxygen. This is possible because of the open areas within the scrubbie. In a submerged setup these areas are filled with water, water which is not in contact with the BB. So using scubbies in canisters creates a sitsuation for bypass, plus per volume the scrubbies have far less surface area when compared to Biomax, ehfisustrat, or even matrix.
In a Fx5 there is alot of volume so using scrubbies would probably work fine, but in a smaller canister why would you trust your fish on media that you saved a couple bucks on?