- The photo reference sources are not from satellites, but from airplanes, so they are from an era older than you'd expect.
Unlikely. One of the missing buildings dates back to before the Wright Brothers. Hell, it dates back to before
Matthew Brady. 
Also, the clarity and resolution of the picture(s) of my house and the anomalous downtown area (less than a kilometer apart) are absolutely identical with no discernible stitching or variations that could indicate different sources, and about five kilometers further away in the uninhabited mountains there are cumulus clouds seen from a considerable distance above them.
- The photo sources are simply wrong; some kind of location misalignment, or photos from a completely different city.
Not possible. Ajijic is a small village and I know it well. You could give me a blind test, show me a picture of the blocks with the missing buildings and I would point out to you "There is Bancomer, there is that big warehouse I've never been able to figure out what it is for... but where is the church tower, there's the plaza but why is it all full of trees?"
It is a puzzlement.
tanstaafl.