To reproduce:
- Add several dock windows and hide some of them.
- Save the layout.
- Load the layout, the windows are not hidden

Workaround:
string strLayout = File.ReadAllText(@"..\..\layout.xml");

foreach (DocumentWindow dw in radDock1.DockWindows.DocumentWindows)
{
    if (strLayout.IndexOf("DesiredDockState=\"Hidden\" Name=\"" + dw.Name + "\"") != -1 && dw.DockState != DockState.Hidden)
    {
        dw.DockState = DockState.Hidden;
    }
}