Without intimate knowledge of either 2015 or 2016 models, if that is the only difference between them, just buy the 2015 model which surely you can get for hundreds less than the newer model. How many $$ could repositioned thru-hulls be worth? (not much, I'd guess)
Depends if the old position is below the water line and hence subject to potential leaks or not. Though as far as i am aware the AI wasn't a problem. But I would eyeball that before making a decision.
I believe the repositioning is on the deck, as the transducer fits in its little cave underneath, while the wires come up to the deck. It is the positioning of the thru-hulls to take these wires inside the hull (and bring them out where the fish finder is located) that I believe is changed. So no difference to the seaworthiness.