This technically isn't a bug (although it wasn't intentionally introduced) and could be considered a feature (see this
forum post).
Other than the superscript suggestion (not trivial to implement), we haven't identified a better way to indicate the presence of Item Notes so we are inclined at this point to leave the current behavior. The "virtual" Item Notes attribute is readonly and can't be deleted, so you still must edit notes in the Item Notes field, but it clearly indicates the presence of notes and can be used for efficient searches (Advanced Search with a criteria of: Item Notes Exists).
Thoughts?