It makes it easier to tell them apart. . . to be sure each is eating. . . to be able to medicate certain ones. . . to know which one is being bullied or is the bully . . . makes it easier for the customer to tell them which one they want, etc.
I find breeders more commonly mark their tortoises and pet stores do not.
As Yvonne says, to monitor which is doing well, and also to identify which one is being picked to be sold. From a photo you can pick number 3, or the blue one!
In the UK and all over Europe, I understand that each tortoise needs to have its "papers" in order. There must be breeding records and permits and such, so each tortoise needs an ID mark. That is how it was explained to me in Hamm Germany at the big show.