Hey Markus, I ran into this issue today as well. Not sure if you have been using built in controls or if you built your own navigation, but I found you can fix this by checking the following when you are writing out your links.
if ((smn.IsPublished() && smn.ShowInNavigation) || (smn.ShowInNavigation && smn.NodeType == NodeType.InnerRedirect))
The first part of my if is checking for published items that should show in the navigation. The second part is checking for Inner Redirects that show in the navigation.
It might be possible to extend PageSiteNode object to add a method that would do this check for all items that should show in the Navigation.