I’m wondering whether there is an easy way to avoid make to try to rebuild cocos2d-x, box2d and stlport?
Of course, make observes that there was no change so it skips the actual compilation, however it is still pretty slow because it has to check hundreds of files.
I’m very certain that build_native.sh will NOT clean the project each time, it only compile the edited sources after your lastest build,
unless you call
./build_native.sh clean
to clean the libraries.
And about the building speed, cygwin is the slowest, compilation on mac osx will be much faster. It depends on the operating system & your hardware speed 
I think you’ve misunderstood something. I don’t clean the project and build_native.sh does not actually recompile any of cocos2d-x, box2d or stlport, however, make still checks for changes in order to determine whether there is need for rebuild and this checking what takes quite some time.
I know cygwin is much slower than linux or mac osx gcc (roughly 5x when using gcc and make based on my experience).
However, I’m searching for a solution to simply skip the makefiles of cocos2d-x, box2d and stlport after the first build as I don’t plan to modify them.
This way the checking of the dependencies can be skipped thus reducing the compilation of my project at least by 3 times.