Basically, an internal combustion engine is cleaner than the human body.
It is easier to extract chemical agents from the water than it is to remove biological agents.
Does that mean a powerboat does less damage than a kayak? I am not sure; I guess it depends on how wet the paddler gets in the kayak. Potentially, an “all day” trip in a kayak would be very damaging (compared to power boating). I am talking 8 hours of kayaking….no breaks…just paddling all day…
So the argument of kayaks being less of an impact on the lake might have a few “leaks” in it.