Our shop works the same as @dayswithaY.
You're right that we can't always tell when a particular item is stolen but we can narrow it down to a particular time-frame. So, if a delivery of seven pairs of size 10 jeans arrives on a Monday, we sell 2, and by Friday we only have 4 pairs, we know one pair has gone missing, presumed stolen. So we can narrow it down to that time period, if that makes sense.
We do mini stock checks everyday, focusing on a different area of the store. I know we have certain items that are more likely to get stolen, so those are checked more often than others, but every item is checked about once a month on average.
We don't have a lot of thefts - we have a small shop and enough assistants on the shop floor to keep watch. We do things like count items in/out of changing rooms, take things off customers when they come out of changing rooms, make sure we fold items at the till so things can't be sneaked through inside other things etc.
I think the key is good customer service, enough assistants to monitor the shop floor and obviously good security. This is generally much easier in small but open-plan shops!