I have a Jackson Cuda and I found the scupper holes are almost the perfect size for transducers. I threaded mine through some PVC to give me an 'arm' for grabbing, wrapped that in some foam from one of those pool noodles with zip ties and it forms an almost perfect snug-tight and level fit on the underside of my kayak. It's really no big deal to add and remove it when I'm launching. Bonus was being able to use the leftover noodle to make a couple homemade buoy markers.
The only negative to this is the need to run your wiring into the hold for the battery and back out again for the finder. Given just how much space and access the Cuda has though, I honestly never notice the wires at the top once I've tucked all the slack up, and the center hatch just sorta sits there on top.
I looked into various ways to run the wiring more seamlessly or permanently but I couldn't find anything I liked. The ability to completely disassemble the fishfinder, transducer and battery to me is far more value than the two minutes it takes me to assemble it each outing.
I'm not sure what I'd do in your case though without some sort of scupper holes, if not available.