Almost without exception, when someone refers to a specific length boat, it is the length at the waterline. Even in the full size stuff, the dimension they discuss is the length at the water line. This is because the waterline length is related to a concept in physics related to the natural speed of the hull. A typical advertisement will say One Meter RC sailboat, so the boat is one meter long.

If they give the height of the boat, I would assume it is from the bottom of the keel (keel bulb) to the top of the mast. If they give mast height, it will be the height of the mast from the attachment to the boat to the top of the mast. Another interesting figure is the sail area, usually reported in square inches (or possibly square centimeters I guess). There are even classes that are reported in two numbers, NN/YYY. The NN number is the waterline length and the YYY number is the number of square inches of sail area. This permits development of new designs rather than "One Design" classes. I prefer one design racing. Builders often prefer the other system.