Just some food for thought:
If it is difficult to see Moodle as a single API, one approach for managing all those APIs would be to actually make them different projects. This is for example how the Symfony framework is doing it: http://symfony.com/blog/symfony2-components-as-standalone-packages
Each API would then have their own version number, and each third-party plugin could define the exact APIs and API versions it requires.
The API projects would naturally need to be included in the main project. One way to do this could be to use composer (https://getcomposer.org/doc/00-intro.md). A simple "composer update" command would fetch and install all the correct API versions automatically.