Lowrance makes a special epoxy for mounting thru hull transducers.
I bought some back in 2005 or 2006. Back then it had a silver metallic quality to it.
See:
http://store.navico.com/products/000-0106-98
I am still using this kayak and the original transducer install is working without any issues.
Why put them in water boxes or create complicated mounts when this special transducer epoxy made by Lowrance specifically to mount their transducers works? I can't imagine they would recommend a product in their installation instructions that would degrade their unit's signal. Maybe I am missing something.
Since you have to purchase 6, I ended up sharing 4 with other brethren. All reported the same success.