(Continuing this topic, which is closed.) [moved]
I noticed that the Remove Unused Objects Tool doesn’t show some of the notes that appear when I filter the Notes view on those that have zero references. I realized the ones missing from the tool’s output were all of type Link (in which I store URLs of records I’ve found online; I attach these notes to citations, in addition to attaching images).
I found that the omission was the outcome of issue 9688, and that also appears to be when the type “Link” was added, though it seems that some other meaning of “Link” was being discussed there.
Anyway, if you are using notes of type “Link”, and wish to find out if you have any unused ones, you can create a custom filter in the Notes category view the rule "Notes with a reference count of 0".