Actually the thru-hull doesn't have to be higher, and an air bubble shouldn't be an issue if the tube isn't vented to air. When the boat is in motion there is a low pressure zone aft of the stern tube ahead of the prop (which is pushing water back). That low pressure pulls water into the tube. (Higher speeds = lower pressure, so they spec a water source on higher speed boats so the tube doesn't suck air.)

Link below.