On the subject though, doesn't AmigaOS3.9 have an inbuilt defragger like Windows?
No.
Also, I asked on another thread if the Amiga had a disk-surface scanner like the MS-DOS ScanDisk/CheckDisk but noone seemed to have any suggestions...
Not that I know of. Anyway such scanners are mostly useless, as current IDE/SCSI drives map the damaged areas internally. If the damage shows up in actual scan, the hdd is ready for scrapping already.