Something you might try before cutting your through-hull. If you're running a fiberglass boat, you might be able to shoot through the hull without losing much in the way of power.
Generally the place to spot your transducer is in the bilge to one side of the keel. This area should have no flotation or wood to interfere with the signal. Place the transducer and level it, and then complete the connection by adding some water to cover the bottom of the transducer. If it works OK, then epoxy or silicone caulk the transducer in place (without the water). Both materials as well as fiberglass are invisible to sonar. As long as you don't have air pockets in the fiberglass, you should be all right.
I used to run fiberglass skiffs this way, and it's a vast improvement over hanging something off the stern.