Our morality is mostly innate. He may not have though consciously about moral values and such. He also may not feel any need to chase after afterlife fantasies via ancient books of fables.
One has to have some moral foundation to function in our society. He seems to be functional, so maybe there's nothing to worry about. Does he subscribe to the golden rule or some variation thereof?
If he's going off and killing for profit or whatever, then maybe being in the military has sabotaged him a bit. That happens. If this is a case, I don't see this as an issue that has much to do with religious belief.
Finally, in your post, I don't know who "an atheist, that is secular humanist who cares about morality" refers to. This forum has postings from believers of all stripes.