Why is a theory even necessary regarding the Koopa kids? Is procreation such a taboo Mario topic that it is inconceivable that Bowser may have fathered children? I say, his private relations are none of our business, and we should just accept the fact that the koop kids have a mother somewhere, which we will probably never see.
I can't imagine that Bowser would be a very caring father, so he probably just abandoned the seven koopalings after they were defeated several times. As for Bowser Junior and the mini-koopas that appear in the Mario Party games and SMS, they are probably just more of his children. Being younger than the koopalings, it is understandable that they look very similar to each other (most babies look very similar to each other, especially to us, another species), and Bowser probably just didn't care enough anymore to give them names.