Hi hazelcs, I don't know much about fragile x, although I do occasionally support a young man with the condition who is in his late teens and attending college.
I'm pregnant with my second child, I come from a family where over 50% of my generation (myself included) have fairly severe birth defects. Although it is a constant worry that my second child will have something wrong with it, I'm glad I know that this is a possibility. Knowing about my family's medical problems, means that my partner and I can be slightly prepared for the worst, and better informed and that the medical staff taking care of me and the baby are aware and extra vigilant.
There's no good time for news like this, but if it were me, I'd rather know now and not feel it had been kept from me - If you don't tell her now, when will be a good time? when the baby's born, a week old, a month etc? This is just my opinion though and its up to you, I know you're just want to protect her, and I wish you all the best.