Hi, polka 
!
It seems related to Muted categories should not hide Tracked/Watched topics, where a change was made:
Other changes have been made after, so the code isn’t the same anymore, but it fixed the similar issue for categories.
I can repro the issue you describe:
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Mute a tag
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Track or watch a topic having this tag
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The topic doesn’t appear in Latest. When a new message is created, it only appears in the New tab, but not on Latest.
Right: posting on the watched topic having a muted tag.
Left: the notification only appears on New, but the topic never appears in Latest.
I feel the behavior should be the same as with the categories: if I mute a category and then track or watch a topic from this category, it always appears on Latest.
It seems like a missing feature, but feels more like a bug because the behavior is inconsistent with how categories work in this regard, so I’ve moved your topic in bug.