It could be either because they were purchased at an outlet or to prevent them from being returned to a store. I guess one way to tell is whether the style is older (meaning it might be from an outlet). Just a guess.
Or, as in bags with labels crossed out -- from a return center of a department store. Stores like Saks will take returns of items they don't intend on selling again. They turn around and get rid of these returned merchandise at their return center, selling them for about 1/2 retail. Many ppl on ebay buy from return centers and then sell on ebay for a small profit. These items will have the labels crossed out.
How could they do that to the shoe? IMO that's kind of like damaging it. It's not like a cheap $20 dollar pair of shoes, it's CL! I know people can't see the black line when you wear it, but I would know it's there and would be bothered. I guess if the price is REALLY good then maybe, but I think they should make a mark with some kind of marker that you can only see under a black light so the shoe still looks flawless.