A unique barcode on the item would be one way to do it, but not the only way.
For example, a common thing to do on conveyors is to have reusable open-top plastic bins called "totes". (Think of going through airport security where you stick your luggage items into a plastic tray or tub that sits on the conveyor as it goes through the x-ray machine.) The totes can have barcodes on them, which can be used to track whatever is inside the tote.
Amazon could use a system like that to individually track items as they're being moved on and off shelves. And while on the shelves, it could track items by position (a database saying this particular item is on that position of that shelf). By combining these two things, they could track the position of individual items without sticking barcodes on them.
I don't know whether Amazon actually does this. I'm just saying it's not impossible.
For example, a common thing to do on conveyors is to have reusable open-top plastic bins called "totes". (Think of going through airport security where you stick your luggage items into a plastic tray or tub that sits on the conveyor as it goes through the x-ray machine.) The totes can have barcodes on them, which can be used to track whatever is inside the tote.
Amazon could use a system like that to individually track items as they're being moved on and off shelves. And while on the shelves, it could track items by position (a database saying this particular item is on that position of that shelf). By combining these two things, they could track the position of individual items without sticking barcodes on them.
I don't know whether Amazon actually does this. I'm just saying it's not impossible.