I had installed some themes, elementary and Aldabra and deleted them in the appearance window. But when I click customize... the window-content and -border of these themes were still showing up. I had to delete the files in ~/.themes by hand. Is this a bug?
It is either a bug, or you had them also in /usr/share/themes. If you don't have them there, then you should report a bug for sure.
I don't think it's a bug, removing the gtk and Metacity themes would be a bad idea, especially when you delete a custom theme. Multiple themes use the same gtk and/or metacity themes, so deleting them would have unintended consequences.