[democrite]

Good idea. Yes please. Maybe some distinguishing mark like an underline (maybe not), an overlay, or highlight style would work but I agree an icon, in the margin I think is the best place, looks to be the easiest and quickest way to identify them. I was going to suggest the minimum margin size, at least in landscape 2-columm be one less than now, but with an icon, 3 less than the current max seems about right. As for type of icon, a pen could work but I believe a plain or sort of plain square, like iBooks and Google Play Books, to simulate a post-it, is most easily distinguishable.

That could relate to my earlier suggestion of no confirmation to remove annotations. A highlight is easily re-added, but a confirmation to delete a note yes.