First of all; I would say it takes some good sized balls to drill a big hole in a perfectly good boat.
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If there is any conclusion to be had at this point, GOOPED transducers are short changing the user. There is more performance to be had with alternative installations.
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I don't know if that's true. I have a transducer in my kayak that shoots through the hull that saw to 3K'(that's as far out as I've ever gone in the ocean); no problems, perfect imaging on a cheap Eagle fishfinder. I also had a much more expensive finder on a 23' Skipjack with an external transducer.
The external transducer was not much more accurate than the one in my kayak; readings were affected by bubbles in the water. Looking at the photos of the transducers removed from the kayak hulls in this thread; there is no doubt the bubbles in the Goop; or whatever it is that was used to mount the transducer to the hull; affected your readings. The key is to apply the Goop; or whatever, slowly and bubble-free; then push the transducer down slowly so no bubbles are created. The end result should be a "thin as skin" layer of Goop between the transducer and the hull. Any air bubbles in the Goop should appear on the perimeter of the transducer as the bubbles are forced out from under the transducer body.
But hey; if an external mount works better; that's great. If you fish in a more remote area; where your kayak is dragged across rocks and logs and non-urban launch sites; anything sticking out of your kayak is not going to fare well.
Depends on what you do.