Some people say to clean out a section of the tank every quarter or so. Pull the plants, gravel vac and replant. I've not done that yet, but the natural ebb and flow of tanks has had me dig up a lot of stuff from time to time.
If roots are emerging from the gravel, I think you might want to add some root fertilizers to draw them back down. If more nutrients are in the water than in the gravel the roots ought to go that way.