Why do aircraft on a junk yard have blind windows (e.g. German "Landshut")?
taken from Business jet news 


  For outside storage, cover windows and recognition/strobe lights with barrier material and pay attention to atmospheric conditions, as humidity will accelerate corrosion. Make sure all control locks or control column gust locks are installed to prevent movement of flight control surfaces.
  (emphasis mine)


One reason to protect the inside fabrics, plastics etc from the effects of discolouration from sunlight, as well as inhibit biological growth. Also without the coverings the temperature inside the aircraft will be significantly higher on sunny days see Desert Usa


  [without protection] the interior could quickly heat up to 200 degrees Fahrenheit during hot summer days