There are all sorts. If you have an aluminum boat you can mount one by drilling a hole through the bottom of your rig and fitting the transducer inside the hole. These come in brass, stainless and some sort of plastic. you will have to pick the one that will not cause corrosion in your environment. They come in flat 10 and 20 degree angles so they can be mounted on the angle of your boat and still go straight down and not sideways. For fiberglass bottoms it is a bit different. Fiberglass has the same reading as water. That means that you can just glue a transducer onto the bottom or have it in a small water reservoir in the bottom of your boat. There is also a type where you drill a small hole in the bottom of your boat and slide the transducer shaft through it. while you have a faring block on the outside that makes it sit on the desired angle.
These setups are not great for boats that are trailered a lot because loading and unloading can damage the transducer that sticks out.
If you want to find out more you should go to Airmar website. They make 99% of all transducers in this country.