I know there is no boolean operations but is there any way to achieve this. I thought of texture projection of alpha texture but this is bad for performance. Is there a way to add polygon to mesh and make it transparent or just flip it or any other technique for creating a hole? I need a simple square holes.

You could of course just splice out the indices for the polygons that you want to remove, from the SubGeometry.indexData vector (and invoke updateIndexData() afterwards.) But then your walls will have to be completely flat and have no volume.

The simplest way would probably be to build your walls from four cubes, one to the left, one above, one to the right and one below the window. That way you can also very efficiently move the window, should you want to do that, by just scaling the cubes (with no need of uploading any new data to the GPU.)