Add the Arc Hydro Tool Bar. ApUtilities is near the right end of the bar.
If you are using ArcGIS 10, I would upgrade to Arc Hydro 2.1. Assign UniqueID is still in the ApUtilities menu in versions 2.1 (ArcGIS 10) and 10.1 (ArcGIS 10.1) for sure. We added it to the toolbox but did not remove it from the toolbar.
Christine Dartiguenave
Esri Water Resources Team