A few things that would make notes and note icons better. None of these are big issues (issues like getting hyperlinks automated on Windows would be much more important) but here are a few issues starting with the least important and moving to the more important.
1. When you append a note with an icon to a Bible verse and that verse happens to come just after a non-Bible text heading, the note icon appears in front of the non-Bible text instead of in front of the verse number. Example:

This makes it appear as though the note is for the entire section covered by the heading and it looks a bit ridiculous if you have non-Bible text turned off:

This has been an issue in Logos since forever, but it would be nice if this were fixed.
2. Allow us to create our own icons.
3. Allow us some presets to resize the icons so that they aren't as obtrusive (or are more obtrusive if you prefer).