About 2 years ago, we started using Trello for project management and then Slack for discussion. We have found exactly the issues you describe. In specific, we have a channel called “QA” — for “Quality Assurance” (it is a software company, in this case) and this channel has become the overwhelming catch-all for every conversation about anything related to QA. In some cases, it supersedes or even replaces our GitHub issues. Many conversations are tangential and — by the olden gods — we often say “thanks” or “yeah” after so many comments, it becomes untenable to follow in any real way.

Slack needs threads. People need discipline. Obviously, one of these solutions is possible (hint: it’s on Slack).