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Can't be worse than how Slack manages Slack threads.

https://github.com/wee-slack/wee-slack#threads

Basically as another channel. When a thread is spawned or someone comments on a thread (and checks the box to echo to channel) then you'll see a thread ID (which is usually three characters).

If you type /thread <3 chars> then weechat will open a buffer in the thread which makes it appear as if it's just another channel basically. Albeit with no name other than the randomly assigned 3 chars.