They're the rivets holding the handle on. In that position it's impossible for them to do any damage to records. It's the ones holding the latches that are the ones to look out for because they are face on to the playing surface of the record, and on my boxes they are covered with felt.
Not sure what boxes you've been looking at, but here's a pic of some of my collection. If you look closely, you will see that each and every one of them has the catch in exactly the same position as the ones I've had made ie downward motion. All these were made in the 50s and 60s, ie tried and tested