When a Stack Exchange site stays in readonly mode, bounties are active, despite the fact that the questions can not receive any response. I think the bounties should be made inactive during readonly mode - they should be stopped and shouldn't expire.
The bounty is paying for advertising the question, not a guaranteed answer. During a read only event, you're still advertising your question.
And most read only events only last a few minutes. One exception to this was the recent UPS outage where Stack Exchange was either down or in read only for three hours. But even then, sites enter and exit read only without much fanfare.
In the end, the purpose of the bounty still happens in read only mode. And I'm not sure it's really worth the development effort because the admin's have poured a lot of effort to keep the sites online.