Is there any tool, script, or plug-in for InDesign or Acrobat Pro that would detect or highlight overlapping characters or diacritics? See sample below:
No, there is none and never will be. I my native language (Latvian) there is also some cases, when I would like to have this possibility. But much easier way is to make a sting of capitals with diacritics and copy it in two lines (again, Latvian alphabet): ĒŖŪĪŌĀŠĢĶĻŽČŅ. Then check leading with lower values from alphabet: qypģjķļņ. That's it - you have a correct leading.