By hiding the ones with unused messages you implicitly tell which ones have new messages because those are the only ones that are visible. It works quite well and enabled me to passively track dozens of channels without being overwhelmed.
As to mentions and highlight words, I don't think there's a solution for that for muted channels. When I developed this technique I would have liked targetted mentions, but not @here or @channel, which, at the time was indistinguishable. However Slack added a per-channel option to Ignore notifications for @channel & @here, which means I might try the above technique without muting the channel.
Play around with it, you might find the settings can be combined in an optimal way once you understand how they all interact.
As to mentions and highlight words, I don't think there's a solution for that for muted channels. When I developed this technique I would have liked targetted mentions, but not @here or @channel, which, at the time was indistinguishable. However Slack added a per-channel option to Ignore notifications for @channel & @here, which means I might try the above technique without muting the channel.
Play around with it, you might find the settings can be combined in an optimal way once you understand how they all interact.