Yes, bounties can be awarded to community wiki answers. The restriction on reputation gain applies only to voting. See this Meta post: Does bounty apply to a CW question?.
The thread linked in that Meta post was subsequently deleted (visible to 10K users). It had 5,472 views, the question had 34 upvotes, it received 62 answers, the accepted answer (and bounty winner) had 109 upvotes. And it was the poster child for an off-topic question (hence the deletion).
BTW, the deleted thread raises a related question on bounties: What happens if a bounty is awarded and the answer is later deleted (does the answerer get to keep the bounty)?
Answer: When an answer that received a bounty gets deleted, all reputation including the bounty are revoked, and the bounty is not given back to the user who awarded it.
- Exception: if the answer had a score of at least 3, and was visible for at least 60 days at the time of deletion, the bounty award is kept.
- Recent new exception: If the question is deleted (taking the answers with it), and the bounty is not retained by the answerer per the previous exception, the bounty is refunded to the offerer. See Changes to bounty rules: removal of double rep-retention, blocking of owner deletion
For a comprehensive explanation of bounties, see: How does the bounty system work?