I know that in 4.5 there are problems still with notes, but at least they are now actually usable for the first time since Logos 4 shipped. Until recently, they tool was so slow and unbearable that I didn't bother. I just spent the morning using Logos 4.5 and kept all my study notes in Logos rather than another program. I'd like to see a few improvements, but I can now use notes attached to a verse and include long bits of information in many paragraphs without it bogging down to the point of making me want to pull what little hair I have out.
Thanks!