When I permanantly mounted my transducer to my new boat, I cut off several feet of extra cable that wasn't needed and spliced it back together. It works great, although the spliced part is not in the water.
Make sure when you do splice it, that you wrap your repair in aluminum foil before your final waterproof wrapping. This is "shielding" that will help keep any outside electrical radio frequencies from leaking into your wires and giving your unit errent signals.
So, you want good wire to wire connections, soldered is best, then heat shrink tubes around each of those, then foil shielding, then maybe big heat shrink around it all, and then I'd use Marine grade GOOP brand to seal all of that from the water. But that's just what I would do. GOOP is really good stuff. My Father in Law was the company's jet pilot until he retired two years ago. He has a free lifetime supply of GOOP products, delivered right to his door whenever he wants it. Way cool ! I've used the stuff for years before I ever knew him.