It might've just been a technical error or an overlook in the plot because there doesn't seem to be a reason otherwise. You're right that Snake wouldn't risk Emma with Vamp. All we know is that the reason he didn't take a shot is because the game would be much easier that way. For the reason why he didn't leave is mindboggling because I wouldn't think Hideyo would be careless like that. Is it possible something was in his way?