The name of van Kooten, of van Cooten, van Koten has likely it originated in the village Cothen in the province of Utrecht in the Netherlands.
There are many families in the Netherlands with the name of van Kooten, who is no relation with each other.
My grandmother is Cuneira van Kooten, she was born in Amerongen, a village near Cothen.
Her genealogy goes back to Jan Roelofsen, born in 1630 in Amerongen. He first used the name "of van Cothen" in this genealogy.
But there are many different "branches" of Kooten,as wel in the North Netherlands and also in West Netherlands.
In my research I have no Jewish connection to explain.