I just went through this with my boat last year. I transfered from CA to WA. If you buy and live out of state for 6 months you pay NOTHING.. but if you move in state within the 6 months you pay the difference in state/s tax (they call a water use tax) and no they don't care what you paid for it, they go by the NADA value. Heres the kicker, the DMV don't know sheeet about this and will try and argue with you, its a totally differnt dept you have to contact. In my case I had to actually get them on the phone and they had to explain it to the DMV.
They have this law because they found with OR having no sales tax people were going out of state and buying big tickets items just so they didn't have to pay the sales tax.
So to put it simply the answer is yes they will have to pay a sales/water use tax based on NADA value BUT you tell them the condition of the boat and they don't care about anthing extra like stereo, ballast, custom blah blah, blah.