Hi @berrakbalci ,
What you are asking here is probably more for the unmethours forum than this one. Or you could probably find your answer by digging through the EnergyPlus Input/Output Reference.
If I had to guess what is going on, it looks like this section of the Input/Output reference is probably what’s causing the cooling load to go down with 100% transmittance shades:
Shading devices are assumed to be opaque to long-wave radiation no matter what the solar transmittance value is.
So, even if all of the shortwave solar energy is getting through the shade, the longwave sky heat exchange is still blocked, which is what you would expect for most transparent materials like glass. I imagine this would lower your cooling load by a bit compared to a case with no Shades at all.
Hope that helps.