The HDSi transducer will not work as an inside-the-hull application due to the Si sonar beams radiating directly out of the sides of the transducer. You would have to mount the standard transom mount HDSi transducer on the outside of the hull or use an XPTH-9-HDSi-180-T transducer which is a true Thru-Hull transducer. This transducer mounts through the hull via a hole in the hull.
Now if you are also getting a DualBeam only (2D only sonar) transducer than yes they will work as an inside-the-hull transducer. I suggest you look at using our MHX-XMK Kayak Mounting Hardware for this.