Ceyan, what do you mean humans can exploit being able to collect bounty? It was mentioned above to have your ally cancel your alliance, blow up one of your planets, and then ally with you again. Sure, it would lower your bounty. It also blows up one of your worlds. Isn't that what you were trying to prevent by lowering the bounty?
Remember I offered a much less damaging solution. Imagine just not being allied and setting a shipyard to build several cheap scout frigates with a rally point right where your partner has a row of gauss cannons built? You lose a cheap frigate you can mass produce without any major economical impact and get your bounty reduced while your partner gets a free source of cash. Best of all, nearly full automated.
Additionally, if you can assign a bounty to yourself, you could work out a team partnership where one person focuses strictly on the economy and one focuses strictly on the military side of things. The person using the economy assigns a bounty to himself, letting the military player collect on it as a source of cash. Requires some extra micromanagement, but could be a devastating combo if the military player is quick on the draw. If you can't assign a bounty to yourself, that'd take three people and probably be more cumbersome than worthwhile.
Likewise there are other combinations like that. Assigning a huge bounty to a player just as an ally launches a massive attack. Not really an exploit per se, but definitely pushing the barrier of fair play.
Of course that stuff could be done through trading resources, but the method I listed provides some level of anonymity (unless someone is paying close attention to the bounty levels).
I've got several other ideas that might work, but I'd have to play with the system more to fully understand how bounties work and are collected.
@Ceyan What level bounty have you gotten up to, I remember a game that I was playing where I had a pirate fleet that was bigger than my entire empires fleet attack a world, we're talking something like 40-50 ships with a nice assortment of siege, anti-sc, rogues, and pirate heavy cruisers. It is the only time I have seen an AI in the game use a sensibly varied fleet composition. The only way that I beat it off was that I just happened to be staging my cap ships in the same system for an attack and luckily the pirate attack phased in before my caps started charging for the jump which let me set them up for an ambush.
I don't remember any specific numbers off hand, but I've been keeping to small/short games so I may not have seen bounties enough to call forth a bit fleet. Still goes to show that the early fleets need some tweaking so they are challenging and not just a reason to build a few static defense or leave a small force in garrison.