I think Commodore introduced this policy as they did not want people to access hardware directly and use only OS provided interfaces (likely same reason for the Mac).
I think this may have been part of it. The documentation existed though and games were using AGA functionality.
Commodore may just not have had the money to publish the HRM. The OS3.0 documentation came on floppy disks, I can't remember if there was any AGA documentation on them.
