They do it to curb sharing of multi-day tickets, which is prohibited by their terms & conditions. It's a relatively quick way to check that the person who first used the ticket is the same person who returned with it, rather than someone they sold/rented it to. Selling or "renting" multi-day passes for some fraction of their days is a common way to make money in the areas around theme parks (and a common way for people to try to save money getting in). I don't think this is all that sinister.

I personally would rather have thumbprint scans than have to wait as each guest's photo ID is checked every time they enter.