I've got my Emacs set up to display in "bold, fluo foregound and a dark background underlined by a pink line" (yes, literally that obnoxious) any character which is not part of a list of characters I consider to be acceptable. And it's configured to show any "zero width" character as if it had a width. So any "invisible character" as well as any "invisible zero width character" does appear as a black square, underlined with a pink line.
I've got my Emacs set up to display in "bold, fluo foregound and a dark background underlined by a pink line" (yes, literally that obnoxious) any character which is not part of a list of characters I consider to be acceptable. And it's configured to show any "zero width" character as if it had a width. So any "invisible character" as well as any "invisible zero width character" does appear as a black square, underlined with a pink line.
And that for any buffer/file.