Does the data layer have anything to do with React or is it pure JavaScript/CoffeeScript project?
It doesn't depend on React, it includes Alt flux stores and actions though - we keep app's state in them, if you don't need them just nuke stores and actions folder and alt-instance.js.
(b) Is the data layer able to work "on its own", i.e. without the UI layer? If so, what is the best way to try it out?
Just create your own test app, import ChainStore.js and play around with it.
(2) Would you be so kind and describe briefly the workflow of the GUI? Especially, I'm curious about these aspec
Look at ChainStore.js and its init() method. We use BindToChainState decorator to connect React components to ChainStore.
This will be a really stupid question: how do I launch this JavaScript CLI?
Goto cli folder and type: npm i && npm start
Please note that cli is slightly outdated and don't use ChainStore that is now official way to query blockchain state and bind it to React components.
(4) If I wanted to run the UI step by step in a debug mode, do I need to have it compiled locally with Nodejs or will it be enough to debug the production code hosted on OpenLedger?
If the former is true, does the whole thing compile on Windows? I've had some problems with it.
For development, run it locally using "npm start" command in web folder, no point to use OL compiled js. It should work on windows but I think it's not tested much.
(5) In the Environment section of your README file you mention those system variables:
I think you can skip this step.
(6) For educational purposes which repository would you recommend me to use: cryptonomex/graphene-ui or bitshares/bitshares-2-ui
cryptonomex/graphene-ui is the primary source, this is where all the development happens, so it's most up-to-date.