It seems once a clan enters a war, all bounties on said clan member are removed. Also no new bounties can be placed on any member of a warring clan. I agree this is how it should run. Although the problem with this, if a clan goes to war to remove their members bounties, they can still retaliate and bounty others.
If a clan enters into a clan war to avoid a 'bounty' war, they should not be able to remain bountying others if they cannot be bountied back.