"Keeping a bounty in your belly is a good way to keep them nice and secure... though it's certainly not safe. Well, for the bounty, that is. For the bounty hunter herself, it's not her problem if her prey succumbs to her belly. The Galactic Federation accepts digested remains as proof, so Samus isn't going to hold back her acids on her target's account. If the target's lucky, a short trip might see them regurgitated so they can serve their time in jail. A long trip, and those acids will get too strong... And they end up serving a life sentence on Samus's chest."