Hello Saar,
Indeed you found your culprit, but added to that I see a lot of transparency objects in your design. If you have many layers as your design does and each of those has transparent objects in them I can imagine that things got a tad slow. Instead of a simple integer being used to display a single colour every layer of transparency needs to get calculated, added to the the previous one using floating point calculations.
I imagine that this is handled on a logarithmic scale 1,2,4,8 etc. per layer used or per overlapping object. If your bottom layers were masked stacks of the same type of objects, I can imagine that the calculations of the masks are applied after going through the whole object stack calculation. Maybe using clips instead would make the result faster as well as those are simpler calculations to my knowledge.
In any regard using lots of floating points explains the delay in screen refresh as well. It certainly isn't the amount of nodes.
Cheers,
Jelle