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Actually, its the ebook reader, either software or device, that enables notetaking and not the file format.
The Kindle devices and Kindle for PC, their software app for Windows, allow such notetaking. I presume, though haven't personally used, the other Kindle for ... software readers will do the same.
These notes are associated with a particular instance of the word or phrase selected. Should the same word or phrase appear elsewhere, the note will not be associated with it. That is, if you encounter a phrase in chapter 3 that is the same as one in chapter 1 that you annotated you won't be able to directly access that earlier note from the instance in chapter 3. You would have to access the notes from the menu and scroll through the list until you found the older chapter 1 note. This isn't hard at all, but could be a bit tedious if there are lots and lots of notes.
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