People were talking about her voice, but honestly I think the reality is that Mitsuki doesn't talk enough to Aya at school for Aya to really have evidence to piece together "hey, record shop boy sounds a lot like that girl from my class."
The way I see it, we needn't analyze too deeply. It's like debating why doesn't Lois Lane ever realize that Superman sounds just like Clark Kent.
My father explained that to me as a child (a looong time ago), it's the fact that Lois Lane is a feather-headed idiot (he used FAR harsher language). For proof of this you only needed to read the comics to see her get warned, usually by Superman himself, to stay away from something/one and she would run straight to him/her/it and get into trouble, then have to be saved by Superman. Over, and over, and over.