CHKDSK doesn’t actually check the disk. It checks the volume which is carved out of a logical disk which is presented to windows. In the case of a mirror it would only check for bad sectors on the active disk, assuming that the RAID controller only allows for reads from one of the disks in the morrir.
If the RAID controller allows for reads from both disks in the mirror then all bets are off. When working with arrays it is better to use the array controller (or SAN) to check for bad sectors as the controller has access to the physical disks and can check them one at a time.