Boats sink even in situations where they shouldn't. I get why a boat should sink if you sail it under a waterfall that has a vertical fall, but we tried building a lock where we added one layer of water at a time and it immediately sank the boat all the way to the bottom. There are crazy workarounds using pistons, but a lock should be able to raise and lower a boat. (Although, if I can figure out how to break the boats to move them around in the system I might be able to use it as a way to drown mobs that get stuck in boats.) Only tangentally related, every time one of our minecarts goes past one of our boats it sucks it up and gives it a ride around the track. The boat being in the water doesn't seem to make any difference. Unless you want boat drowning systems it seems the best system would be something like - boats sink if they are under more than one block of water. That would let a lock raise the boat, and sailing up shallow water flows, but not steep water elevators.