I think the cause of your confusion must be that you are viewing language exclusively as a way to communicate information. Because of that, you look at the two sentences and ask yourself "how is the information different?" That is the wrong question. The information is not different. The two sentences say the same thing. The difference is in the mind of the narrator. In #1, the narrator thinks about the scent as something that happened further in the past than in #2. This would only matter to you if you cared how the narrator thinks. Normally, when you read a novel you do care how the narrator thinks. Why would you read the novel otherwise?

They both mean the same in colloquial speaking. The first is using the had structure. The second is using a shorter lazier structure that is common in English colloquial speaking. The first sentence using had = the smell of brine that had been left on the pillow (in the past) is still lingering and can still be smelt. The second sentence = the smell of brine is still lingering on the pillow. They are just changes of tense and perspective being used to mean the same thing.

Confusing