Roots getting darker is not root rot. It could be a lot of things though, and the first sign of root rot. Are they slimy, is your reservoir slimy? Is there a funky odor? Is your water warm? Lot's of great threads in here to prevent these things and to find what is appropriate or not. Sometimes nutrients change the color of your roots, usually it's water temp though. I have pretty limited DWC experience, but I know enough, lol. Anything with a lot of carbon in it will change root color, carbon will also attract disease, so be sure you are either keeping your reservoir sterile with h2o2 or something similar. If you want to grow beneficial bacteria to help feed your plant and fight off the bad bacteria, you need to make sure you are hosting the proper environment and feed your good bacteria (also eats carbon). Look up Heisenberg Tea here on RIU, you'll learn a lot.
Carbon, Carbohydrate, remember your plant and bacteria see these as the same when digesting it, and carbon is crucial to growing bacteria and sweet heavy buds.