Realistically you're not going to see every single object in a room, especially, smaller objects like keys and books but if you examine certain items like shelves and desks you'll see even more objects like books and keys... keep in mind these are not containers but have objects on them.
Would I simply just make the objects that are on a shelf invisible and turn them visible when the object that it is located on is examined..

I made them a surface container and ticked the boxes 'hide children...' and 'list children...'.

Then, when you look at the object, they will appear and be listed as a 'child' of the shelf/desk.

I'm always puzzled when I see questions like this, until I realise that unlike most people, I choose not to auto-display objects, etc.

Not using any panes and choosing to include all the necessary information in my description, makes things so much easier. Although I accept such a minimalistic style is not to everyone's taste.

I feel so dumb, didn't realize the container feature also had an option for surface container as well.

No worries! About 99% of the questions I ask I think are dumb, especially when I hear the answer!