Copy-pasted my answer from StackOverflow, since I could answer it for myself.
So, I finally managed to resolve my issue, and it was way easier than I thought. Instead of going with the c++ source modifications, I found a function in the Cocos2dxHelper java class which is the nativeSetApkPath. After investigating the use of it, it turned out that Cocos2dx handles the apk package as a zip file. Since my obb is just a renamed zip file after all, I could use it without any problem. All of my assets were loaded fine, except the sounds. Which requires another quick fix.
Most of the credit goes to a forum post (http://www.cocos2d-x.org/boards/6/topics/11243) and to Irwin Billing, since that was a base I could use for my modifications in the Cocos2dxMusic.java and Cocos2dxSound.java classes.
Also, I had to be sure that the sound assets were not compressed in the zip file (according to the documentations provided by Google).
For that I used the following command on my Mac:
zip -rn .ogg:.mp3:.wav assets.zip assets/
The last thing I’d like to mention is the folder structure. I copypasted and zipped the assets folder, so I have a folder inside my zip file. Which is great, since the apk works the same way, I had to do no more modifications.
Finally my modified source files, just dont forget to go through it, and change some values