I'm having (sort of) the same problem, though I'm running Arc Hydro 2.1 on ArcMap 10 (build 2800).
Using Fill Sinks from the Arc Hydro toolbar works with no problems, but when I call FillSinks in the ArcHydroTools module:
ArcHydroTools.FillSinks(AgreeDEM, Fil, "", LevelPoly, "ISSINK_YES")
I get the execute error "System.NullReferenceException: Object reference not set to an instance of an object."
Unlike the post above, FillSinks fails to complete.
I've tried using an integer (1), a string ("1"), an expression ('"ISSINK" = 1'), etc. in lieu of using ISSINK_YES, all to no avail.
The command is part of a script that automates a number of other Arc Hydro processes; all work without a hitch, save FillSinks.
Has anyone found the correct way to use the ISSINK field in a script? Am I missing something simple?
Thanks!