Boats are scheduled for the update after the next (Conquest Update comes out today, Morale Update probably in January, then Boat Update). Bridges will be coming in the Morale Update, but those will be restricted to settlements for now. You'll be able to use them to cross rivers, but not oceans. I'll see about tweaking the "small landmass detector" when picking start locations to give a better warning about islands.
For the disappearing settlers, when you order a settler to settle in a region that already has a settlement they should vanish and join the settlement as 1 population. Are you not getting the population increase in the settlement?