I built a flat bottomed lapstrake canoe a couple years ago and I did not add runners to it. I did glass the bottom both inside and outside though. I painted it with good ole rustoleum and it still looks new. You could add runners to your kayak. They shouldn't affect how it handles, but as noted, they will slightly affect how it handles in moving water. As long as you aren't dragging it around on rocky beaches, not much will happen. I have found that with my Kevlar canoes the bow and stern bottom is the only thing that gets a ton of wear. You could add a layer of Kevlar tape to just those two areas and you should be fine. Some canoe outlets offer a kit just for that. I am currently building a SUP board for my wife. The plan calls for 4 oz glass on the bottom and I doubt that I will do anything beyond that. My main concern is that she will knock the skegs off at the boat landing. And if she does, its nothing that a little goo and glass won't fix.