I've never installed a shoot-thru transducer. I've only ever done the transom mount or through-hull. But, I *think* you need to epoxy it in place? In that case, yes, you'll want to get to bare fiberglass.
My concern was more about whether or not you have a double hull. I didn't think your model did, but I wasn't sure. If your bilge floor has "bumps" on it (not perfectly smooth like the topsides) then you're good to go.