Wow, that's slow. My 3000T with Cyberstorm MK3 '060 and Mediator scans 2 SCSI buses and reboots twice with the latest BoingBag updates and still boots in less than 30 seconds. One thing you can do is turn off multiple LUNs and disable any SCSI addresses you don't use if you have SCSI settings for this. Also, you can set the flag for the last SCSI unit/device in the RDB with HDToolbox or a similar RDB tool. I believe HDToolbox does this automatically when you run it but you must click on the last hard drive (by SCSI address) and then click save changes to hard drive. Other RDB tools allow this to be set manually. Setting this LAST_DEVICE flag keeps SCSI addresses after that from being scanned on bootup. It's especially handy for SCSI CD-ROMs, scanners and zip drives that do not have a RDB and should not be scanned. You want to have all your SCSI hard drives at the lower SCSI addresses for this to work and having your boot hard drive as address 0 speeds up things also.
P.S. The LAST_DEVICE flag may not be the correct name and I've seen it called different names in different RDB programs but I think you get the picture. Someone will be along shortly to correct me ;-). I'm not on my Amiga right now or I would look it up.