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.
I mean, they did actually address that in the 1978 Superman movie - there's a change in the way he speaks and his body language when Clark Kent becomes Superman. It's neat to watch in motion though.
I imagine it's a similar deal for Mitsuki, hence why the times where Aya feels like "She seems like the guy at the record store" Mitsuki's doing something that's uncharacteristic of how she usually acts.