Motoko has several modes of vision, so I suspect she'll be able to tell fairly quickly that things are not real, because...
...

...well. Some things just don't look right. I mean she hasn't got ranger eyes like Batou, but still. Yes?

Of course, there's also that everything is different from before and also insane and jRPGish. That's a bit of a clue-in. This is going to be interesting.