I believe those boards are stiffeners for the deck kinda like a spine. The deck doesn't sit on them but the deck is just nailed to them. I had my decks out on my 99 a year ago and the construction was identical and they were still solid with no rot.
AD41P-A and DP-D1 outdrive about 800hrs. Extremely efficient boat for her size, Fish OFFSHORE all day on less than 30 gallons of offroad (tax free) diesel. This Boat is set up really nicely with second station on roof and lots of shade coverage/metal work. I have seriously gotten offers for it...