From FME2018.0 it is possible to collapse bookmarks. Maybe it is an idea as well to collapse annotations into an icon. It would be nice if you could choose between two or three different icons, for example an exclamation mark, a question mark and a ligthbulb. The different icons (maybe it should be possible to manually add them) can be you used to distinguish between the type of annotation
Open
Collapse annotation
+10
+1This would be extremely helpful! Especially when workspaces start to get large. Being able to click on a transformer and pop out an annotation.....yes please....