This should be in the Hardware Issues section tbh. You have also omitted a lot of information such as;
How many other SCSI devices are on the chain?
What SCSI devices are they?
Is termination set correctly?
Are the devices SCSI jumpers configured correctly?
Afaik, the Amiga 3000 was not capable of Auto-booting from CDROM without being configured in some way or other. I do know some big-box Amiga Accelerators do allow this Auto-Boot from CDROM & OS3.9 will, providing you boot from the Boot Floppy first!
Tbah, Termination is probably slowing you up, so be sure both ends of the SCSI chain are terminated. You may also have to shuffle the Devices positions on the SCSI cable in order to Gel things correctly & if you are running External SCSI Devices as well as Internal, the SCSI Termination guide can go entirely out of the window!