I've had this happen on a number of occasions now when bounty hunting. I've taken a pirate ship down to zero hull when it was charging up the FSD and then they enter supercruise. Normally when they hit 0% hull there are a few secs before they actually blow up. During these precious secs they escape and presumable blow up in SC (happened to me once), but no bounty is gained. For the big ships I usually target the power plant, and smaller ones the thrusters because they sometimes can outrun you. I like the delayed blowing up sequence, but it would be nice to claim the bounty too under these circumstances.