Node.js multi platform project structure
This is an highly subjective question. But Meteor is what you are looking for. It does support desktop, browser, mobile, etc. and encourage NoSQL by it's native MongoDB support.
As a reference, I personally did try every single one of the frameworks you have tested (Sails, MEAN, etc.) and ended up with Meteor as my preferred.
As for the project structure, you can read more on various tutorials, books and YouTube videos. The learning curve is steep, but the community behind the project is quite alive and helpful.