There's similar problems with the Traders and Prisoners bounty missions too; a complete lack of clarity over what constitutes a valid kill.
After some trial and error, I discovered that Type 9s in USS instances count for trader kills (Wedding/Funeral barges, the ones that offer to buy stuff, etc.), but I'm still stumped as to what a bounty hunter or prisoner ship is.
It's got to the point where I just ignore those missions now. Hell, most of the time if I'm looking to make money bounty hunting, I just camp out at Nav Beacons now. Much more profitable.