If you haven’t already, I would start by downloading the files, buying a kit of parts, and making your own OpenFlexure microscope. That will give you a greater insight into the aspects involved than you can get from the online resources (great though they are).
Some initial thoughts on your questions:
As @WilliamW notes, the number of ‘downloads’ doesn’t really relate to much: you could have an individual who downloads, and then builds a microscope from it, or a company which downloads it once, and makes a thousand. And lots of downloads which don’t result in builds because they were bots, or were people who haven’t got round to it yet.
While it is not strictly essential, many builds of the microscope will likely include a Sangaboard to control the motors. I am not sure whether the data on this is commercially sensitive ( @filip.ayazi ?), but it may be possible to obtain the sales numbers for this, and with suitable caveats that may act as a proxy for build numbers (and the trends over time may also be informative).
Manufacturing costs are easier to quantify (side note: CNC machining isn’t an option for this, it can only be FDM 3D printed). Many newcomers to 3D printing look at the amount of filament used, and erroneously base their costs solely on that. However this will be a small fraction of the overall cost, as there are many non-printed parts you need to include, and there is also the depreciation on the 3D printer and the everything associated with the workshop environment used, plus of course the costs and time taken for assembly, testing, certification, sales, marketing and delivery.
I guess an underlying question is clarifying the title of your thesis, “Return on Investment…” ie who you are looking at to gain the RoI? It is the end-user who is benefitting from obtaining a lower-cost alternative, or a manufacturer who can undercut the competition? One of the drivers behind the development of OFM is reaching markets that could otherwise not afford such devices at all - so in areas where it is not just an alternative to ‘standard microscopes’, but an alternative to not having one at all.
Good luck with your thesis. I for one will really look forward to reading it.