Yes, the roots will decay. Just like in nature. I personally have done this many times with no problem so far. Even with clones sometimes you have to remove a plant. I use 5" net pots filled with rock in my flood table. The roots grow out and are exposed but they get shaded by the plants and I have no problems with it. I like to use the net cups because I can move the plants around the table as I add and remove plants. I harvest a few plants every week and add more. I try to keep my plants small so I can harvest an ounce or so every two weeks from a 3x3 table.