Interesting speculations. However, I'm struggling to wrap my mind around the concept of a futuristic birth-control method that's perfectly effective at eliminating monthly hormonal cycles without side effects, yet somehow still not effective at preventing actual pregnancy!...
Nothing's 100 percent reliable. The point is, if she'd been using it without incident for years, and it then happened to fail at just the wrong time (or if she let it lapse, like Ben Sisko did with Kasidy), then she wouldn't have noticed "lack of period" as an anomalous symptom.