I would not take a kayak at all on the SJ, but if I was going to take one on the Yampa, I sure as heck would not take a long boat. What is the point? To race down to the next campsite?
Just above the confluence, there is a world class hole that is big and fluffy and worth hiking back up to two or three times.
Still, I think the best route to go with a low water Yampa trip is a ducky or a short raft. My next choice would be a short kayak. The last thing I would want to be stuck in for five days is a big hog that is not designed to play in. Again, what would be the point?