Whenever there were two same class/type ships sunk but reported both of them in different tonnages, I assume U-boat captains measured waterline between target's draft marking of their the hull. Here's link, & look at picture of draft marking.
http://reference.findtarget.com/search/draft%20(hull)/
So you see if a ship carry nothing, then waterline would be much lower, but if carry full of oil, then waterline would be much higher. But for storms, captains can still estimate close enough since storms usually rock ships with empty or light cargo more compare to ones with heavy or full of cargo.