I'm keep rethinking this now... I thought my transducer was gonna fit inside the grooves running along the scuppers but it is just a tad too wide. Might have to build something that can easily be removed for transport.....

I was going to do the scupper mount but my transducer wouldn't fit in the groove so I opted for thru the hull. It worked pretty good but eventually broke loose. After the third time I mounted it on the stern. Now I can store my rods inside the boat. I do need to refine the mount a bit (maybe with a spring as Pelican has done his) cause mine as it is now is always getting bent around or a limb popping up between the boat and transducer. I may go a hinged route. Like this http://palmettokayakfishing.blogspot.com/2011/08/diy-kayak-transducer-arm-for-2012.html?m=1

Anyway here is mine as of now

Is it crazy to thing the transducer o. The front of the yak would be better since you would cast into it? Just thinking out loud

I had mine over the side for at least a year and then switched. Now it's bonded inside the bottom of my yak (Hobie Revo 11) with Marine goop. I'm much happier with it inside the hull. I haven't noticed any change in the performance of my sonar unit, I don't have to remove and re-install it all the time, it isn't making noise dragging in the water, it isn't in the w, I don't snag anything on it, and I'm not worried about damaging it.

Here is the video I watched that showed how someone could mount it inside the hull. Its actually in part 3 of the video's just to save you some time if your interested. This was my original plan, but now I'm just not sure, it does seem to be convienent and safe from damage.
http://youtu.be/TwcKZG8h7jI

No issues on any of my yaks shooting through the hull. Been doing it for years. The temperature readout will be accurate after a short period as the hull assumes the ambient water temperature. I usually have reliable readouts in 10 - 20 minutes, depending on the disparity between the air and water temperatures.