Rolf,
Yup you have a mess. Suspect that when you installed ArcGIS 10.0 you may have allowed it to install Python to the C:\Python26\Arcgis10.0 directory rather than performing a Custom installation omitting Python 2.6 (and then using your existing PtyhonXY installation).
Believe your PYTHONHOME and PYTHONDIR varaibles are keeping ArcGIS Desktop functional with PythonXY--but suspect the installation of ArcHydro picked up the partial ArcGIS10.0 installation from the ArcGIS entry in the Windows registry.
You can verify that by checking for a residual registry key (only used by Esri's installer/uninstaller) pointing to HKLM\SOFTWARE\Wow6432Node\ESRI\Python10.0, if it is there it came from your Desktop10.0 install.
Suspect your additional folders in the C:\Python26\ArcGIS10.0\Lib folder are probably left over from the ArcGIS Desktop10.0 installation. Is your HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\ESRI\Desktop10.0 -> Desktop10.pth registry value set to C:\Python26\lib\site-packages\Desktop10.pth or to the default C:\Python26\ArcGIS10.0\lib\site-packages\Desktop10.pth. If so, to make your PythonXY functional you would have had to copy the Desktop10.pth file to the PythonXY site-packages instance.
Also, what are the time stamps on the folders in the C:\Python26\ArcGIS10.0\Lib directory? Do they coincide with the earlier Desktop 10.0 installation, or with the ArcHydro install? I don't think the ArcHydro installers includes a Python build, so probably have always been there.
The ISSetup.dll is the module of the ArcHydro installer that does the Python detection, it is possible that it has been altered to reject anything but Python 2.6.5 and NumPy 1.3.0, but I'm more inclined to think it is a combination of residual ESRI\Python10.0 registry values affecting the installer.
For me when ArcHydro is installed against an alternate Python, it only creates the C:\Python26\ArcGIS10.0\Lib\site-packages\ArcHydroTools.pth file--this is a hardcoded installer action.
If you clean out the incorrect Esri C:\Python26\ArcGIS10.0 residuals from the file system and Windows registry, you should get a complete installation of ArcHydro 2.1.0.132. But, you may need to specify a "PYTHONDIR= C:\Python26" running the ArcHydroTools.msi installer from a command prompt. Then simply copy the C:\Python26\ArcGIS10.0\Lib\site-packages\ArcHydroTools.pth file to the C:\Python26\Lib\site-packages directory.
Stuart