Doesn’t make much sense to me either, but it’s possible that just like Kelly’s blue book for cars is sometimes just off, could be similar for NADA? In real life boats just don’t depreciate this drastically unless there was a major change. It would concern me from a resale perspective, if that factors in for you. If not, I’d go with the boat you just like better which seems to be the 2006. I would have to defer to others to talk about the differences between the years, hopefully smart folks come along. Good luck with your purchase.
2002 Supra Legacy
1991 Alumacraft Lunker
Old Town Discovery canoe