I wouldn't try to cut a transducer or GPS cable unless you are skilled at that sort of thing. I'm an electronics technician in the Navy Reserve and I've been trained to make up and repair small gage data and coax cables......and I wouldn't do it. I don't have the tools or materials at home to do a GOOD job of it. I could easily splice a coax cable, but I don't think that I could do it without some signal loss or noise. I don't like having to coil up 25' of cable inside the hull, but I think it's better than a bad connection any day.
I think that the answer is leaving the FF mounted. Back when I had a secure storage area for my kayak, I never took the FF off. Now I leave my kayak on my truck all the time, so I have to take the FF off and lock it up. On the old yak I just used a good coating of dielectric grease and covered the head unit with a marine electronics cover and I never had any problems. I would only need to take the head unit off occasionally to clean and re-grease the connectors. A ziplock bag or a marine electronics cover will protect the head unit and connectors from splashing water. A cover or bag won't keep it dry if you are punching through a big wave, but it will protect it from water being forced through the seals. In five years of kayak fishing I've never had a head unit fail due to water penetrating the case.
You can see the marine electronics cover in the image above. I got this cover from Boater's World. It has a couple of small vent screens on the top to limit condensation build-up and fogging. The cover has an elastic bottom that keeps it firmly attached. I've gone through many a wave and I've never had it fall off. If you're using a ziplock bag, you can put a large rubber band around the neck to keep it in place.