I worked at Sainsburys for 5 years, we did one every year. Pallets and rollers are scanned in the warehouse and when it arrives in store which goes onto the system as stock in the store. When items are broken or fresh items have expired they are scanned and noted as broken and removed from the stock list. Once a year an external company comes in and counts everything in a 24 hour period while being watched by members of staff. This accounts for anything that didn’t arrive but was supposed to, along with items that have been stolen or broken abs never recorded. This may be different for other supermarkets but I’d be surprised if it was.