When you turn it off underwater it doesn't suck water up thru the headers. At the very most it'll fill your muffler(hopefully not the cat too) once you start it tho you usually just blow it all out.
Generally you don't want to use the clutch underwater. It won't guarantee any issues, but it does increase the chances of damaging the clutch.
I'm a little more timid with deep water. If i know it has a good base and can get thru it ill go through seep stuff. If I'm uneasy, ill let my friend go first haha