This gives us a natural filtering mechanism for community input. We regularly sort this by number of upvotes. It also lets our users submit some off the wall ideas, and gives a way for low friction community feedback to be captured. Finally, it lets community members easily be notified when a feature is delivered by subscribing to the issue.
We also have a separate, private list of commits to customers. (The commit is public and is added to a milestone, but the customer is private.)
We also group issues by theme[1]. It's not perfect but it's an attempt to make sure we don't run into the duplicates issue you mention. It allows the eng team to address multiple issues in the same area of the code at once.
I understand what you are saying about clutter, but the low cost public feedback and tight loop between issue and code is worth some issue creep, IMO.
0: https://github.com/FusionAuth/fusionauth-issues/issues
1: https://github.com/FusionAuth/fusionauth-issues/issues?q=is%...