If you want to have an idea if an ML probably does actually like you, ask yourself two questions:
a) Do girls in real life usually like you?
If yes, she probably does. Or if not,
b) Do you act differently with an ML than you do with girls in Real life?
However, as you said, part of an MLs job is to be flirty with customers. This is part of her service, which we enjoy. But obviously, if she's trying to see you outside, she doesn't just want you to be her customer.
But the only way to truly know if she does really like you, is by seeing her and having an affair with her outside the shop.
I say, who cares if she does or doesn't ! enjoy it and assume she does like you! You're the one paying for it!