I have an Elite 5 DSI that I brought over from my Pro Angler 12. Solid unit. I shot through the hull, although I was warned that signal would be degraded. Not true. Perhaps in 1000ft+, but that's a really long haul here in the Gulf of Mexico. The screen still looks just as stellar as when it was in the water.
With that said, I have heard that Sidescan cannot shoot through hull for obvious reasons. It scans sideways on a broader angle out of the transducer. While I like the mod above, I sail with a fishing partner when going on offshore fishing trips. I just could not see giving up a MD well for a transducer, as once there is a hookup the sail is furled and pedals come into play. Similar is the case for nearing a wreck of structure. The sail furls and its pedaling to hold over the structure for bottom fishing. It could be addressed as well but I would be terrified of ripping the transducer cable somehow in the heat of a battle. YMMV of course.
I did see a mod that I was very close to doing. Looks nice and tidy with minimal modification. Give it a look as well. http://www.hobiecat.com/forums/viewtopic.php?f=11&t=43697