It's OK if the root systems have grown large and together, that's normal. If I remember correctly your system is a flood and drain system. So unless the roots are growing into the feed or overflow lines, you shouldn't have any flooding/watering cycle issues. If they are, just clean them out. But if you try to pull some of the plants out of the tube now, you wont be able to without cutting the roots off. That will leave the plant's dead root mass in the tube. The dead and decaying root mass will feed pathogens and fungi that can cause root disease for the living plants.
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