Like I said way back when this whole bounty discussion started, the other reason for bounties could be to collect bodies. Oro showed us that you can create terribly powerful slave zombie warriors (that even sounds cool) by simply having the rotting corpse of a powerful ninja and then sacrificing any nameless minion of yours to power it. So, you can simply place a bounty on some asskicker ninja, have him taken down by an uber powerful bountyhunter like Kakuzu, and you have a weapon to use in some special operation. Nothing personal but extremely efficient compared to devoting 20 years to raise a ninja that still might not turn out well.