I was able to debug using gdbserver with breakpoints successfully by doing the following on Mac with Eclipse.
But, it depends what version of cocos2d-x you are using, because the buiild_native.py was changed after 3.4.
The issue with v3.5+ is that Eclipse needs to kickoff the build_native.py and the new v3.5+ uses the cocos command. There is probably just an environment or path issue, but I have not resolved that yet.
But if you use v3.4 then the above way to debug android code in eclipse should work.