C++ – Using Environment Variables in Visual Studio 2012

does it make sense to incorporate all libraries into my project e.g. in _3rd_party_libs_ folder ?

Do whatever you want, but keep it consistent. I do note that you've listed examples such as boost/sqlite; these should be standard in your dev environments and not included in your project, unless you depend on say some funny version of boost.

how to handle lib include paths in my modules (environmental variable, relative paths, git submodules, etc. ) ?

This is what your build system - CMake - is for. Your source code just has #include <third_party_lib.h> without worrying about where they are located.

should I always build external libs from source or just used their binaries ?

Prefer binaries by default, unless you have a good reason to build from source every time.

It looks like size of your client is important.

From Visual Studio 2013 and MSDN Licensing Whitepaper - November-2014 page 10:

"Example 2: A Fortune 500 firm has outsourced the development of its store-locator mobile application to a small agency. The application is not an open source project. The agency has 5 employees working on the project and would like to use Visual Studio Community 2013. Since the agency is a contractor developing this application for the Fortune 500 firm, and since the application is not an open source project, the agency cannot use Visual Studio Community 2013 for developing and testing the application. "

So your small team can't develop customized app for big company. Don't know what about boxed apps. Don't know what about "individual".

I've done some more research and it looks like small teams can sell apps build with VS2013Comm. There are no restrictions in EULA who can buy it. I guess the key words are sell and outsource. When you sell, it's still your app. While outsourcing, usually app isn't yours but clients. That's my story and I'm stickin to it. Let me know if you think I'm wrong.