If it is a condition that a doctor is treating her for, then you need to report it. Even if the treatment is just aspirin or similar. If it is a condition or symptom that you are self diagnosing, then unless you are a doctor, and you're determining this because you spent time on medmd.com, then its not really a condition. You have to determine if its truly a health issue. If you believe it is, then you need to get her looked at. If it is truly a condition that a doctor has diagnosed, then yes, it can affect her chances of getting into the academy, ROTC, or enlisting. Because of the nature of the military and its mission, it can't have people with conditions that can affect their ability to perform at a moments notice. You can't call time out in the middle of a battle. Its not like a medical condition that you can plan for, like a pregnancy or even a menstrual cycle.
But the only way you'll know for sure is to apply. The military will let you know if its a disqualifying condition or not.