You should definetly transplant those. They are planted pretty deep in those pots or take them out and put a fresh layer of soil at the bottom of the pot. I usually leaves about 1/2 - 1 inch showing on the inside.
But, If I wear you I would get a bigger pot and transplant. The size of pots you have work real well if you are going to flower a clone about 1 week after they root.

Hope this helped any.