It would be great/nice if they have it at the store.
「お店にあったらいいね」は英語に直訳したらこのようです。
It would be great/nice if they have it at the store.
直訳ではないですが、I hope they have it (at the store) や I hope the store has it! も言えば自然です。
「お店があって欲しい」の意味です。
☆お店にあったらいいね。もし置いてなかったらどうしよう。→ It would be great if the store has it. What will be do if they don't have it??
★絶対あるはずだよ。→ They definitely will have it./They certainly will have it.
ご参考までに。