I have used a couple different methods on different kayaks, both work well. One is to use a suction cup mount and stick it to the side of the kayak as low as possible (keep it level). Just be careful when you get near shore or any obstructions to avoid damage to the transducer.
Another method is a shoot through the hull idea. I took a plastic soup container, like you get from a Chinese restaurant. Cut the bottom out of it. Use a product called Plumber's Goop to glue it to the floor ( I put it behind me on a Wilderness systems SI kayak). When it sets up, it will be watertite, mount the transducer to the lid of the container. Fill the container with water, set the top/transducer in the water. You can easily take it out to take it home/inside. This method works better for me because I was always bouncing the suction cup deal off rocks/stumps or whatever. The transducer has no problem shooting through the hull.
J Franco might have some ideas, or know of a mount you can buy, I just like the safety of mounting it out of harms way.