I've only had one actual close call with a kayak on the water as most around here seem pretty good about keeping themselves visible, but there's one guy on a lake I fish a lot who likes to take his kayak out in the evenings right out in front of his place. The problem is, his place is right next to the boat ramp and what compounds the issue is as the sun is setting he completely blends into the silhouette, with his dark colored kayak, his dark clothing, and lack of light. The first time I ever saw him out, I had shut down already, but I was only about 40 yards or so from him and despite paying attention to what I was doing that was the first time I had seen him because the angle changed enough that the background was a little lighter. It could have been closer, but it was more along the lines of "What if.." that made it close. Had he been further down the weedline I may have run him over. Now whenever I fish there in the evening, I shut down way earlier to avoid any issues, but it's because I know there's a chance he's there. For someone who doesn't have that information it could make for a bad situation.
As important as it is for boaters to pay attention to avoid any possible situations that could arise, it's equally as important for kayakers to make sure they remain as visible as possible also help avoid these situations. They sit low to the water and can easily get lost in the waves at any distance.