や lists a few nouns as examples — “A, B and so on”. と gives the complete list.
はこの なかに てがみや しゃしんが あります。
In the box there are letters, photos and so on.
つくえの うえに ほんや ノートなどが あります。
On the desk there are books, notebooks and the like.
や picks a few items and implies there is more. など at the end of the list makes that explicit. Compare と: 手紙と 写真 = letters and photos, nothing else.