I think the premeditated running of waterfalls is far less of a risk than historical canoe tripping in the arctic, especially in times before satellite communication. I've heard of waterfall jumpers breaking a leg or getting injured, but I don't think I've heard of a death. Many, many canoeists have died on arctic wilderness trips over the years.
Waterfall jumpers are usually highly expert whitewater paddlers and safety experts. They probe the plunge pool carefully for depth and obstructions, sometimes scuba diving it. They have safety and rescue boaters in the pool. Probably the greatest risk is going unconscious on impact, which is one reason for safety boaters. Thousands of incompetent paddlers have gone on wilderness canoe trips.
Running falls is just another aspect of paddling sport, and it's a maturing niche. It's interesting that open canoeists are now running higher drops than the kayakers were not too long ago.