In all my years of practicing, I have never seen birth defects result from the "It was before I knew" indisgressions. As long as the indisgressions stopped as soon as the mom became aware of the pregnancy. The above noted substances are obviously not optimal for anyone's health, but most likely have not caused any significant harm to the baby. It will be important for your ex to be frank with her doctor, about what she used, is using, etc. The doctor will probably order an ultrasound to check everything out. These scans are usually done at about 18-24 weeks. If she was my patient, I would NOT recommend terminating the pregnancy based on this history alone.
I hope you are supportive in addition to concerned as that will help her stay away from "trouble" during this very important time!
There could be chances for birth defects because she did it in the early stages. ):
Don't worry though, most of the time you're baby will be fine.
Just keep her away from all those retarded things.