@oyvind tags and aliases are two separate things. Anything you include in the tags: ["tag1", "#tag2"] will show up in the tag pane. Aliases go under aliases: ["An alias for my note", "An alias with a symbol not allowed in file names?"], etc.
@melsophos I don’t believe links are replaced by the alias unless both filename and Alias are exactly the same. The only way you would be getting replacements is if you selected the alias as during linking using [[.
If there are further questions, please open new threads in #help.