-nya is used as a possessive for a person or object where it is already clear what posser we are talking about (outside of I or you). Saya Sri owns the pencils in question, and it is already clear that we are talking about pencils that belong to Sri 'pencilnya' would be used. Just as with asking about prices. If asked a shop keeper how much they sell apples for you would ask "Berapa harga apel?" but if you had already established that you we looking to purchase apples and then decided to enquire about the price, you would say "Berapa harganya?" (how much it ITS price)
The frustrating part is that you cannot tell from the sentence whether they are referring to ONE pencil or MANY pencils. The quantity is ambivalent in THIS particular context because usually Indonesians put a quantity in front of the noun or some type of qualifyer like "banyak" or "sedikit". I think it's confusing for new learners to understand that this sentence is automatically referring to "many" pencils.
Indonesian is not a very specific-obsessed language like English. Basically, if the context demands it, use the plural, "pensil-pensil dia".
Otherwise Indonesians will just avoid using plurals in day to day conversation. As for the translation, as people as just learning, they really should use the plural if they give the answer as plural.