A couple of years ago there was a discussion about the possibility of replacing download-deps.py with a git submodule of cocos2d-x-3rd-party-libs-bin. It was rejected because the size of the repository history is fairly large (as it handles binary files).
There is a recent feature since git 2.10 that allows shallow submodules which would solve this issue. It could replace download-deps.py, config.json and the zip files with a new entry in .gitmodules
path = external
url = https://github.com/cocos2d/cocos2d-x-3rd-party-libs-bin.git
shallow = true