A: "Would you like to have some juice?"
「ジュースいかがですか？」

B: "Do you have any apple?"
「りんごのある？」

A: "Yes, we have the apple one."
「リンゴジュースあります。」
soa natural?

A = natural.

B = it sounds a little bit strange. If you were in a very casual situation and said "Do you have apple?", the person would most likely understand. However, it's more common to just say "Do you have apple juice?"

A = not very natural. It's better to say "Yes", or "Yes, we do." or "Yes, we do have apple juice."

In Japanese, I think people try to shorten their sentences a lot, especially when the subject is clear. However, this isn't always done in English. For example, we always say "I" in our sentences, whereas in Japanese it is better to leave out 私, so just be a bit careful :)
If you want to stay on the safe side, just include the subject.