I have two different areas for different transducers. The first and my primary is a through hull and the second (side imaging) is mounted on the side of the Jack Plate.
Have mounted them at the base of the hull just above a "level" strake before. I prefer the 'through hull' method as opposed to drilling a couple of holes in the boat. (Have done it that way before and never had any problems as long as you use marine grade silicone, just my preference)