Because it's not an acronym. It's an administrative designation code for the office. While many are acronyms, others are not. The key is to make sure they are unique across the agency. They are in effect tied to mail distribution in large government buildings. It's a lot easier to write AIR-130 than Aircraft Certification Service, Engineering Directorate.
Once you get out of headquarters, the regional/local offices tend more to the standard acronym for the office: Aircraft Certification Office (ACO), Flight Standards District Office (FSDO), Manufacturing and Inspection District Office (MIDO).
If you dig through the FAA organization you'll see that the major office codes have two common properties: they all start with an "A" and are three characters long.
While Air Traffic Organization (ATO), Human Resource Management (AHR), Commercial Space Transportation (AST), are at least an approximate acronym; Airports (ARP), Finance and Management (AFN), and Aviation Safety (AVS) are more of an abbreviation.
Flight Standards (AFS) and Aircraft Certification Office (AIR) are under AVS.
As to why AIR was chosen, I can only speculate as it was done a very long time ago and from experience in other government agencies, when these are set it's typically some staffer to the front office that proposes the structure and the boss signs off on it. So at most you'll find a directive that says what it is but is unlikely to specify the rational for each.
Personal speculation would be that AIR comes from 'Airworthiness' or looking way back, it was originally the Aeronautics Branch. AIR could be drawn from that or an early mission statement that tied them to 'Inspection and Regulation'. Take your pick.