I find it hard to believe that Apple didn't know. I would expect any device with a in-house app installed to be reporting metadata about said app back to Apple. Comparing the number of installs of a particuler app + the distribution of IP addresses/locations where this app was installed vs that of a normal in-house Facebook app would likely show a discrepency.

Reasons for the contrary (Apple could not have known) my premise is incorrect, the metadata is insufficient, Facebook or in-house apps in general are much more widely use than presumed and often deployed from a public facing servers resulting in a location distribution too similar to the actual US population distribution, etc.