It sounds like the game world will have all objects in a game-specific database of some kind. It also makes sense that you'll have a certain amount of knowledge about all of these (which will vary, depending on what you find out), so that knowledge would also be linked to the relevant database entity. This could include any annotations you wish to add.
If the HUD can display augmented reality, that could include information about, say, a station that's visible through it. Rather than clutter up the HUD with reams of text, it should likely be limited to a few icons representing certain categories of knowledge. However, it should then be a click away from looking up the full details in your journal/library which contains all information you have on everything, including the annotations. The library would be your "front end" to the information in the game database. The HUD icons could include a flashing red one for "Important - look up notes before approaching", in case you need reminded of a reason to avoid or to handle in a certain way.
The adding of annotations would be done in the journal/library by some appropriate method, although normal information could be added automatically as you make discoveries. There are some ideas about a library here
. I reckon the journal and library should be different, albeit linked; the journal should include entries relevent to you, such as missions and status, whereas the library would contain information about the universe. There could be all sorts of settable preferences dealing with filtering and displaying the info.