Firstly, I would like to say that the lack of belief in a God will not harm her in any way or is a threat to her health in any way so I would say drop that. On the other hand, smoking WILLLLL harm her in basically every way!

The fact that your ex knows and is "OK" with it, completely complicates things.

I started smoking when I was 15 years old, and my parents never confronted me about it. I'm not sure if they even knew, because I would come home from school, and would be home alone for hours, and able to "freshen up" before anyone could find out.

If they did confront me about it, I would probably have reacted badly, because who wants to be told what to do when you're 15, 16, 17 years old and think you know everything there is to know about the world.

The best thing you could do I guess, is to educate her on the negative aspects of smoking. Don't tell her "SMOKING IS BAD. STOP NOW". That won't do any good, and she might just want to smoke MORE if you did that.
Have a serious discussion about how it can affect her SKIN (wrinkles around the mouth, yellowing of fingers), teeth (yellowing, falling out, gum disease), cause premature aging and other things like that. You can also mention all of the cancers, but a 16 year old always thinks their invincible to everything, therefore a 16 year old girl would probably care more about her looks than her health on the inside. Telling her all of the nasty things that could happen to her skin and teeth and such (in a short period of time) would scare most teenage girls more than saying "you could get cancer", and might have a bigger impact on her than you think.

Well, that's all I got for ya off the top of my head.
I stopped smoking after 4 years, and let me tell ya, it was no walk in the park. Probably one of the hardest things I've ever done. I quit during the first few months of my first year of University too!
It took a while, but here, 2 years later, I have been free of smoking since!