In response to this question, I was thinking that we should maybe highlight all tags that will be automatically re-mapped to another tag.
We should probably add a Legend on to SO to state what the highlighting mean (similar to the Legend on MSO)
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This shouldn't be necessary.
Tags that are designated as synonyms of other tags should not appear in the system except in the synonyms area (I think it's debatable whether accepted synonyms should appear in the autocomplete, but that's a separate discussion). The only reason why they do appear is because when a synonym is accepted, the existing questions are not automatically retagged.
Tags with synonyms that need merging appear by filtering the synonyms list by the "merge" item. This should make it easy for mods to keep on top of what tags need to be merged.