Sure. I am aware that Scrivener offers the writer a nearly complete solution. I am only using it as a writing tool as a way to separate each section as I assemble my writing. In this way I find it very helpful to control-click the different sections and review how the different sections are flowing together in my writing. I can easily select contiguous or non contiguous sections, so that I can see if I am making the ideas clear that I thought I was making clear, or if I am repeating myself (bad), or clarifying a previous point (good).
At this point I am not using Scrivener for much of what it can do including labels, cork board, or outline view. I stay in scrivenings view, in the shallow end of the pool. I click in the menu bar and do searches quickly throughout my document when I want to find something. I realize that Scrivener can also format its output and, that is probably great. I come from a technical writing background and I used to use Word very well. I no longer feel it is necessary to put up with maintaining a license for Word. Nisus serves me quite well with everything that Word could do. I can’t say it is anything more than sticking with what I am comfortable with.
Just to mention it, Scrivener’s developers also make a very rudimentary mind mapping app, Scapple. I got Scapple early on and have tried to like Scapple but, I just can’t. It is way too simple, IMHO. I found that another app I have takes better care of my mind mapping and list making process, Curio. Curio, like Scrivener, does a great deal more than I am using it for. I don’t have the expertise to go too far into Curio, but it is a great tool for putting together dissertations and other research from a visual perspective as all its work is done on large open whiteboard-like spaces on the Mac.
As to your question of using Hook with Scrivener, you could use Scrivener entirely for your project, place research links in your research area, etc. But if you are working like I am, and you want to access a mind map program from your Scrivener project, use Hook. If you want to access a saved search in HoudahSpot for the associated research already stored on your mac, use Hook. If you use a central project processing and note storing area as I do (I use NVAlt), use Hook.
I discussed my writing process on this forum using Scrivener here.
ADDED: I use a Notes page to link using Hook with Scrivener. Since Scrivener, like most of the apps I use in my writing process (TaskPaper, Nisus, Curio), has no iOS companion app, this is how I make do. I use a specific page in Notes to update with my current writing sample.
I will at regular intervals put what I have written in Scrivener into Notes for viewing or editing on my iPad for a walk about. This happens often in my writing process. I find it pleasant to go outside, walk to a quiet location, and review my ideas. Or, just smoke a cigar while I think (something I don’t like to do at my desk).
I find it useful to hear what I have written, read out loud to me. I actively follow and review the words I have written as they are read aloud and, I often catch errors this way that I would other wise have missed.
I usually bold the paragraphs that contain any edits that I make on iPad Notes so I will easily notice the changes when I resync with my Mac. After Notes syncs back to my Mac, I can copy the changes I just made to the text, back to my Scrivener document.
Or, sometimes I will print out the pages I am editing as well as pasting them into Notes. As I hear the iPad speaking the text aloud, I follow along on hard copy (pages) and I make edits on the printed pages. Then I take those edits back to my Mac and enter the changes individually into Scrivener.