I did a complete "find / -name '*dia*.desktop'" on my notebook and found 
multiple relevant files:
  
/home/niko/.local/share/applications/menu-xdg/X-Debian-Applications-Graphics-dia_(gnome).desktop
  
/home/niko/.local/share/applications/menu-xdg/X-Debian-Applications-Science-Engineering-dia.desktop
  /usr/share/app-install/desktop/dia-common.desktop
  /usr/share/applications/dia-common.desktop

The files in /home/ are the ones, which do not show the application name and 
which do use a low-quality xpm icon.
Changing the icon to another one or creating a new desktop file for an entry 
resulted in the expected behaviours.

I did find similar files for all the other mentioned examples.

Where do this files come from? 
Should they be ignored completely or merged with the global list? 
How to distinguish them from valid entries like?
  /home/niko/.local/share/applications/wine/Programs/ConvertMovie 
1.1/ConvertMovie 1.1 Help.desktop
  
/home/niko/.local/share/applications/cxassoc-cxoffice-8de7bcbe-ff14-4597-9d18-e04dd84067d4:audio_x-ms-wma.desktop
  /home/niko/.local/share/applications/gedit-usercustom-1.desktop

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https://bugs.launchpad.net/bugs/737777

Title:
  dash shows multiple icons of applications

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