My current bog is on its 3rd summer, it is not filled with roots, most bog plants are shallow rooted. I have not noticed any bad smells even when turning it on for the first time in the spring. I filter with only the bog, it keeps my pond in great shape, no string algae, no green water in the big pond. My bog is around 25-30% the size of the pond, full of plants
I do not draw my pond water from the bottom and do have a huge leaf basket before the pump. With a settlement chamber you will be keeping a lot of the debris out of your bog.
My previous bogs, I never had to clean them, one pond ran for 10 years, then I moved, it always had great water.