In terms of who Ganondorf will be able to speak to, he won't be able to reach the high council members, but he will be able to speak to those leading the investigations and issuing the bounties. The following information will come easy enough:
There is a "cross-Armada" agreement between the Corsairs and Paladins when it comes to hunting certain creatures, and whales are on the list.
Because Corsairs don't want Paladins to come sniffing around and discover the other highly questionable and probably illegal activities they do, they're trying to handle things their own way, and that includes setting high bounties because "those idiots, if they want to do something illegal, at least cover your tracks better!" (Should be noted that the person doesn't care either way, just the principle of the matter: if going to do crime, at least do it well.) It's also a good way to show the Paladins that they are really trying to take care of things. (Whether that stops Paladins from trying to investigate is a different story.)
They've managed to figure out a few of the remaining ships and will warn that they are likely heavily armed and capable of naval battles. If they're out there doing a high stakes illegal operation like this, they are likely not going to go without a fight. And despite the official's earlier comment, it was the whales that were their undoing than another ship or organization, so they will still try to employ tricks and evade. Their ships may be large, but they will be fast. Not to mention these are Corsairs, so don't expect honorable warfare.
Whether Ganondorf can turn any of the remaining hunters to his side is questionable. They are a ruthless group, but if they see someone they can align themselves with then they might turn. If you wish to try, we can do a few dice rolls to see how successful he is. (Note: there would be a limit on how many who could join him.)
If Ganondorf tries to question any hunters he captures, they won't know who the identity of their employer is (it is not uncommon for people to use aliases and third parties and less questions asked the better for them), but will mention they always do their exchanges in certain remote islands. A little digging will reveal the islands all belong to someone under the name "Thyme". However, further investigation will be required to figure out who this "Thyme" is.
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Hope this helps!