"네. 서점에서는 책을 파는데 사실 책이 아닌 (네) 다른 물건들도 많이 팔잖아요?"
=> Yes, they sell books at bookstores, but in fact they also sell many different items other than books, don't they?
아닌 is the attributive form of the adjective 아니다 (negator "not", "is not", "other than", the opposite of "이다").
So, as you say, it means "things that are not books".
책이 아닌 다른 물건 is like "different items that are not books", which might appear redundant("different" is not really necessary), but it is often said like this. It may be thought of as an emphasis.
This kind of back-to-back adjectives are fairly common, even without a comma: 차가 아닌 더 좋은 교통 수단, 내가 만든 맛있는 음식, etc.
Also, you're mostly right in what you said, except 책이 다른 물건들 which doesn't make sense.
"Different things than books" can be said in many ways: 책이 아닌 다른 물건들, 책(은) 말고 [빼고, 제외하고] 다른 물건들, 책 이외의 다른 물건들, etc.