For camera bodies without autofocus microadjustment capability, how do repair shops calibrate a specific body and a lens combination suffering from the focus shifts (back and/or front focusing)?
These cameras have microadjustment capability, just not in a user-accessible way.
The exact method varies by model. Some have a software feature in an advanced (and secret) "debug" menu — the Pentax K10D, for example, had this. Others have physical adjustment screws or similar (like earlier Canon Rebel models). Or, repair centers may simply use shims.
To find the exact answer for a given model, you could either dissect the camera and look, or find the repair manual.