At 12, she doesn't need to be worried if her periods haven't started yet. However, any kind of physical stress can stop menstruation, as can weight loss, which can occur with Crohn's. Even if she is not losing weight, if she is not gaining weight as fast as expected at her age, that could prevent her periods starting. Another factor may be medications.
Check her BMI is healthy, and keep track of her growth in height and weight to make sure she is within normal ranges, and monitor for other signs of puberty. As long as her weight and growth are ok, don't worry if her periods don't start for a few years yet. Check with her doctors about whether her medications can affect puberty.
Just try to keep her as healthy as possible, but Crohn's does not usually prevent periods from starting. Even if she starts later than her friends, it's probably not because of Crohn's. She is still very young!