There are really simple ways to play dirty with APIs like making sure that they are incomplete in subtle and inconvenient ways like leaving out some of the metadata. Hypothetical example: make it impossible to query tags on issues. You'd still be able to do most things through the API, but if you have a workflow that's heavily dependent on tags, the data is effectively siloed.
Sorry, I misread the username and assumed you were the commentor I replied to. Yes, these things are _possible_ but there is no evidence or indication that they are happening with Github.
I agree that there are no signs at the moment. Companies change over time, so a certain risk - however small - is present, as with all 3rd party services.
