The nuance of 3:
*The customer already knows that there are books in this store.
*The store clerk is saying that there are books, just not here
In other words,the store clerk is suggesting that [There aren't any books on this shelf, but there are on that shelf] or [I think there are, but not in this part of the store.] Of course, if there weren't any books in the store, the store clerk would have used [ไม่มี] to respond. [อยู่] is used when you know beforehand the existence of a person or thing.
[มี]have
subject(place) + [มี] + person/thing
customer question(interrogative)
1.Do you have any books(in this store)?
(ร้านนี้)มีหนังสือไหม
Store clerk reply (affirmative)
2.We do have books(in this store).
(ร้านนี้)มีหนังสือ
Store clerk reply(negative)
3.We don't have books(in this store).
(ร้านนี้)ไม่มีหนังสือ
[อยู่]exist[is/am/are]
subject(person/thing) + [อยู่] + place
customer question(interrogative)
1.Where are the books?
หนังสืออยู่ที่ไหน
Store clerk reply (affirmative)
2.The books are there.
หนังสืออยู่ที่นั่น
Store clerk reply(negative)
3.The books aren't here.
หนังสือไม่อยู่ที่นี่
An easy situation to get confused by
*[มี] "have" and [อยู่] "be" can be confusing, especially relating to a person's existence or whereabouts.
[Situation]
Ms.A call a company(store, house, etc.)to ask [Is Thomas there?] with the assumptions that he is there.
Ms.A's question(interrogative)
1.Is Thomas there?
คุณโทมัสอยู่ไหม
Company response(affirmative)
2.Thomas is here.
คุณโทมัสอยู่ที่นี่
Company response(negative)
3.Thomas isn't here.
คุณโทมัสไม่อยู่ที่นี่
4.We don't have a Thomas here.
ที่นี่ไม่มีคุณโทมัส(อยู่)
