C:\Program Files (x86)\ArcGIS\Desktop10.3\ArcToolbox\Toolboxes is the location for the System toolboxes - the main Arc Hydro toolboxes are located there.
C:\Program Files (x86)\Esri\WaterUtils\ArcHydro\ArcToolbox\Toolboxes is for the more project specific toolboxes developed as part of projects and integrated with Arc Hydro.
Christine Dartiguenave
Esri Water Resources Team