Hey Marta 
Welcome! I’m a fellow academic, and just chiming in because your workflow matches mine very closely indeed. You’ve already got some really great replies, and I will bracket my own by suggesting to go slow, and keep it simple.
If at the beginning of my academic writing and researching career someone had handed me my fully fledged workflow, I wouldn’t have known what to do with it. Also, having spent so much time building it myself over the years forced me to get comfortable with a suite of complex apps with endless permutations, tweaking things just so they suit what I want to get done (cf. @DrJJWMac 's sage advice: focus on your ‘desired outcome’). That said, I’m sure you have saved yourself some heart-ache by deep-diving into the DT forum, which is a goldmine for academic productivity and where I have probably learned the most (about DT and other apps, too).
Anyway, I’d also suggest to pair things back as much as you can. Spend time on the things that really matter (research, thinking, writing!), and build your workflow from the ground up as and when you need a new complication.
- Don’t use Devonagent just yet, and get comfy first with getting data into DT (via the clippers, import, drag and drop, etc. The DT Manual is wonderful on how to get data in, as is this free e-book: Take Control of DevonTHINK 3).
- Don’t use an external PDF reader on iPad (yet). I tried but couldn’t find any additional value. My needs for PDF reading are modest: highlight and annotate. Working with DT2G has the benefit I don’t need to ‘save anything back’ to the app. All annotations simply sync back to DT on my Mac. I’ve never had any trouble with the PDF framework that @rfog describes, but be warned!
- I use Obsidian for exactly the reasons you cite: keeping a knowledge base of reading notes alongside DT. You could do this all within DT, but in my view, there is less friction and Obsidian is designed as a note-taking app (DT isn’t, despite its immense capacities). I also keep atomic notes, but sort off – there is way too much fetishising of this vague idea of atomicity – I mean, good luck deciding on what is just ‘one’, ‘indivisible’ ‘idea’. But it is very valuable keeping both reading notes (that respect the flow of argument of your source), and extracted from there and in conversation with other notes, what you might term ‘concept’, ‘idea’, or ‘atomic’ notes that cut across your reading and thinking; and which may indeed, as you describe, belong in their own (arbitrary, user generated) ‘thematically organised’ hierarchies.
Your Qs:
1
I sync with Dropbox and it is rock-solid. Bonjour is fine if your machines are routinely in the same room. I would avoid indexing for now until you understand its opportunities and limitations exactly (because messing with indexed files = DT messing with your files stored in Finder).
Keep it simple with Zotero. It’s a brilliant tool. But I only use it as the repository for all citation metadata (NOT PDF storage and annotation), and to generate bibliographies at the end of the writing process. These apps clearly have overlapping capacities, but you don’t need to use them just because you can. I think it’s better to have one app do one major task: file storage (DT); bibliographical data management (Zotero); notes and thinking (Obsidian), even if all three apps allow some of these things to some degree. What is mean is, don’t duplicate these processes across different apps, but rather choose the app you like most for any one process.
Otherwise when I write, I keep my own shorthand place holders when I cite stuff (e.g. Cronon 1991, 22). I expand these only when I turn to Word to edit a draft for submission. That means, then, that I don’t do anything complicated like indexing a Zotero asset library (but you can if you wish).
3
@MsLogica has already given you good advice here. DT shines because every item has a unique location that you can link to it from anywhere. Simply right click any item in DT and ‘copy item link’; or hit ‘edit’ in the menu bar and do the same:
You can paste that link wherever you want.
I get some extra mileage from writing my notes in markdown in Obsidian, and in my taskmanager (ToDoist), which as you may know offers an easy way to format links in this way:
[decriptive text here](link address here).
Here’s a real life example from my Obsidian from something I recently read and took some notes on:
[PDF in DT](x-devonthink-item://03CD1967-1F22-47BA-AD6B-F4C3EE11D9EB)
This is what this looks like in the wild:
The huge benefit is that I can just click the link from Obsidian and the relevant PDF gets opened by DT. It’s MAGIC and greatly speeds up my subsequent working with these notes. Obv you can do the same in-house in DT, which offer some very excellent ways of working with plain text, markdown, or RTF note taking.
Right – this is more than enough by way of info I bet.
Good luck, enjoy the apps, and your academic workflow journey.