This question was recently posed before me, and I wasn’t sure I was understanding the question. There are different facets to it, so I’ll address each one. First, I must make a few distinctions that may be lingering in the back of some minds. When the Christian refers to creatio ex nihilo it means creation out of nothing (material causation). Then there’s creatio per nihilo which is what the atheist wants to affirm, which means creation through nothing (efficient causation). The Christian will affirm creation per (or through) God.
My first take on the question is, “How can God exist in nothing?” And by this I’ll mean ‘in’ refers to a spatiotemporal reality. Also, I want to be clear that by ‘nothing’ I’m referring to the absence of anything unlike some philosophically inept scientists like to do. I’m using ‘nothing’ as the negation of anything. Well, there is no metaphysical, logical, or physical necessity for God to exist in any spatiotemporal reality. God is a disembodied mind. (Three minds, actually.) This is a problem for the pantheist and panentheist but for the classical orthodox Christian the question falls moot unless the object can demonstrate a metaphysical necessity here.