I think it's about how we calibrate our expectations relative to the default. I do think there is something different about smell.

For example, if I wake up one morning, my implicit expectation is for it to be reasonably light because of the morning sun, and I'd expect to hear some low level noise because I live in the city. The other day, I woke up and I noticed it was darker than usual because of terrible weather. Recently, I also noticed it's much quieter than usual near where I live, because it's a student town and many have gone home for Summer. I didn't immediately notice, but I had a sense of uneasiness until I consciously registered this, because I had a subconscious sense of what's normal.

I can't imagine what waking up and there being less smell than usual would be like. For example, if someone came in and tidied up while I was asleep, without waking me. I'd notice it if there was a particularly strong smell when I went to sleep, because as you highlight, people do comment when an expected smell is not to be found. However, because of how we acclimatise to scents, the normal level of smelliness of an environment is often undetectable, so I don't think people would generally notice a subtraction of a background smell.

It makes sense in the context of human perception though, our olfactory system is underdeveloped compared to many other animals because we don't use it much, relatively