If the body fat isn't there, then nothing (not even a dribble, or a delayed/intermittent period) happens. By itself, it's not a reason to assume she knew. I'll throw my personal experience out here - I had my first period rather young, at a chubby age 11, and continued to have them until age 14, when a combination of ballet and eating disorder caused me to lose a ton of weight. (Even at points when I was still really healthy and weighed a muscular 130 pounds [height 5'2], I had no periods, nothing. So it might well be possible that other girls who enter puberty that way don't start until rather late.) The (total) amenorrhea lasted two years, with weight fluctuations of more than 80 pounds. My doctors were never concerned about it unless I was underweight.

They did test my hormone levels at some point for another reason (mood disorder, I think?), and found that I had very high levels of estrogen and somewhat low testosterone. Meanwhile, all through this, other aspects of puberty were basically normal. I don't know if that was the case for Semenya, because I don't know how her condition would manifest exactly... you might be right if she showed no feminine attributes at all, but is that the case? It's difficult to talk about in a public arena.