I break off the majority of roots when harvesting. The really small ones would drive me bonkers trying to do it all at once...so I dump the remaining hydroton into rubbermaid bins a few inches deep, and stack them (in alternating directions) to let them dry out. I will leave them there for the entire next crop. By then, the hydroton is really dry, and any remaining roots are brittle and just break off if you swirl the pellets around a bit. Then toss them into a sink for a final swish before throwing them into the pot for the next round. I keep TWO CROPS worth of hydroton at all times...one to use, while the other one dries out. Just keep alternating use for a crop/dry for a crop, and its almost effortless compared to trying to clean them up just after harvest to use again right away. That's when you can get some potential problems missing old bits of roots or whatnot.
For the price of hydroton and being able to re-use it for infinity, I thought it was worth is to just have double what I needed and do the process above. Saves a tonne of time.