-- Last Updated: Dec-23-12 4:25 PM EST --
Usually, but it isn't just the water line. Each stroke in a too big boat is significantly more and unneeded effort compared to how hard they would be working in a more suited boat.
A kayak (and canoe as well) that is too big for a paddler will be slower because it will not reach its design waterline. Hence the lightweight paddler is not getting the advantage of the hull profile that the designer was planning on.
A boat that is too big will also be hard or downright unpleasant to handle because it will be hard for a too-small paddler to get on edge to turn, maybe impossible. Same for rolling unless it is one of the rare hulls that will behave OK for a huge range of paddlers, like the old NDK Explorer or the newer Nordkapp LV. But a better fit still works best - the Pilgrim by NDK designed to handle smaller paddlers handles more adroitly than the Explorer for its target audience.
Even if the boat is padded out in the cockpit and loaded with shit to hit the waterline, the person trying to handle it will still have to go thru gyrations to handle it rather than just being able to easily and thoughtlessly drop the boat on edge to make it go where they want.
The too-big kayak boat will always be a barge, even in forward motion, hence not much fun to paddle on more aggressive or longer trips. (Though getting someone into a too-big boat is a pretty good way to make them stay home over time.)
But the issues it creates for more adroit maneuvers, especially in a kayak, can be worse. It can make the difference between being able to get a boat turned quickly or not.
As an aside, there are a rather good variety of boats out there now for smaller paddlers, including used. You can do better than a Pungo in terms of features like dual bulkheads etc.