Agreed. When I worked for Borders we were required to have our bag checked at the end of the day. We also had to check in if we brought in our own book, or a product the store sold, and get a sticker with a manager's initials to prove we didn't steal it. But I rarely did bag checks on the sale floor from what I remember (hey, it was almost 10 years ago). Mostly I tried to check employee's bags as they were clocking out, unless we were slamming busy and they had to find me to get the OK.
Also, we weren't actually allowed to touch anyone's stuff, it was just a "hey, here's whats in my bag, here's my special sticker that says I brought this book, ok, see ya later". It was a 10-second process.