i had a thaught about the transparant water. im guessing that this could be achieved by not making the water see-thru but instead changing the water reflection for each boat so it is a upsidedown version of the model.
if you understand what i am trying to say then great, if not its kinda hard to explain.
um, the reflection map is usually the same 3d model as the actuall boat. i havnt tried to do any of this as i dont have sh3 installed atm so i dont know how accessable the reflection map is.
so this is the model \________/
~~~~~~~~~ lol boat on water
and this is the refection map \________/ exactly the same as the model
so you get it reflected onto the water like a mirror
if you flip the reflection model upside-down im guessing that the reflection would be flipped too so with a bit of tweaking you could get it lined up so that the reflection is showing the hull of the boat instead of the masts and stuff reflected
kind of giving a transparant water effect
\_________/
~~~~~~~~~
\__________/ this kinda thing
if anyone understands this or how to do it then do try it and see if it works, i am no where near good enough to attempt it so i wont but thats some input from me