Is there a reason to upvote community wiki posts? Does an upvote on the community wiki matter if there is no rep associated (why waste a vote on it if I can't give credit to someone for a good question or answer)? Is it a waste of a vote?
Voting on community wiki posts is most certainly not a waste of a vote.
There are two ways to look at votes:
If you only view votes solely as the means of punishment (downvotes) and reward (upvotes), then CW votes would be pointless, since as you say there's no rep given or taken away. I prefer to look at them in the second way as I find it more useful overall. Reputation awards/losses on "normal" posts are just a side benefit.
The goal of community wiki posts is to allow editing by the community in order to improve their quality. Lack of reputation changes is incidental.
It affects sort order and influences what responses are considered "best" by the community, moving them up and down on the page.
Users can still earn badges for community wiki posts, if not reputation.
StackExchange uses voting system to make good answers go all way up and bad ones all way down, not to give rewards and reputations to people. (And a reputation system is perhaps a way to rate users as well as give them permissions based on their reps)
Upvoting/Downvoting means this vote is useful/not useful