[quigonkenny]

So basically Ayaka hypothetically read the Nagi report, which hypothetically contained hints to his magical nature (that neither Asuna or Negi thought troubling, considering Ayaka is a mundane), at which point Ayaka kept her new knowledge hidden all though the first leg of the Wales trip, after which she decided to bone up a little more on Nagi (the newer report we see her reading in Wales) and Eva, then came home and confronted Eva out of the blue.

Either that or she's always known about magic.

I don't think so. Highly, highly unlikely. Either scenario. Ayaka may have a little restraint, but she doesn't have a deceptive bone in her body. She would have at least pressed Asuna more for info, had she any idea what they were involved in. And her whole character type ust screams Muggle. Here's what I think happened:

Ayaka is as mundane as the day is long. The older members of her family might be magic-knowledgeable, since any company as large as hers would have to deal with magic in some capacity if it existed (her enrollment in Mahora itself may be to groom her for the time when she has to take over the Yukihiro family and deal with the existence of magic), but she herself is uninitiated. She uses her position to get the Nagi information for Asuna and Negi, then follows them to Wales. She knows something is up, but out of respect for Asuna decides to stay at arms' length and not get involved...until they disappear.

Negi's sister seems unconcerned about their disappearance, but she's evasive about Negi's personal and family details, and Ayaka can be surprisingly perceptive when she puts her mind to it, so she can tell that something is, if not necessarily wrong, certainly not right. At that point she decides that it's more important to help if she can, and to do that she needs information. So she commissions a few more reports on Nagi, since that's what Asuna was looking into, and her family's less mundane resources come through with a lot of...very interesting material. So then maybe she decides to look into a few of the "known associates" those reports reveal, since there are a few familiar names she keeps seeing (Konoka's father, Takahata-sensei, Eva...), and before long she's got a new perspective on life in the Negiverse.

Then Eva calls her back home. At this point she probably knows something is up with the loli vampiress (she's got a long flight ahead in which to do some more reading, so maybe she doesn't know everything), but she holds off on confronting her until she's out of Wales and back home (one of the reports suggested that memory loss charms are pretty common, and thus likely known by Negi's sister).

And that's where we're at now.