I always wondered if the line shouldn't be adjusted to "Why are you... up?" or something like that instead, the idea of the line is that she could be asking why he's standing up in the bath or why he's got a boner. A bit of vagueness would probably help things out.
It's actually implied he hit her in the face with his dick in his rush to jump up. That's why she's touching that part of her face. So, in that case, she'd know about the boner (she's seen it before though, and they're siblings, so she's less prone to absolutely freak out about it compared to the other girls though).
I have always interpreted it as a situation where Rito for some reason had to bathe with his sister but then has a normal physiological action which, to her annoyment, prompts him to suddenly get up which surprises Mikan and with a slightly camouflaged aroused voice she asks him why he had to suddenly physically stand up while she was still talking to him...
In short, she probably knows why he stood up which explains her blushing.