Yes, technically the Kings would have had a salary cap incentive to ensure Buddy didn't make his bonuses, but I doubt they would have had much control over them. He was 21 threes short of Harden, so it's not like there was a reason to bench him at the end of the season to make sure he didn't get there. They'd never even dream of deliberately missing the playoffs to get a salary cap advantage of $500K the next year!
Incentives follow the contract. They actually get recalculated in a trade, so if Buddy were traded to a team that was in the playoffs last year, his salary cap trade value would be different for us than it would be for the team he was being traded to. His contract is big enough that it probably washes out, but it could put a kink in a deal if things went exactly wrong.