you can deduce that there are around 10000+ such squares in that column of the table
I think you need to rethink your design. All the squares are creating way too many DOM elements and that is why performance is bad. Without knowing what your squares are trying to do it is hard to make suggestions.
You might consider using server generated images for the squares or you might consider using expanding rows and only show the squares when the row is expanded.
We have already updated the design such as now the squares are server side generated images. The performance is improved a little, but not as much as we need.
I think we are not going to follow your second suggestion because our users will want to see them all in the same time.
I don't know it this will help, but we make sure that we do everything we can to a store and grid separately and only add the store to the grid at the last reasonable moment. The same goes for updating the grid: I always create a new store and re-add it to the grid.
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