First you should rename the HD0 and HD1 partitions on SCSI address 0 so you get rid of these ".1" names on address 1. Having multiple partitions with the same name can cause heavy problems on other setups.
Second, these "partitions" that you call "LUNs" actually *are* LUNs, not partitions. The Elbox FastATA (aka 4xEIDE) splits large HDDs into 4GB portions and mounts them as LUNs. For AmigaOS each LUN is a different HDD. So you can certainly use any HDD wipe program on this LUN. In order to do least damage, you can use my program KillRDB which just changes the RDB id. This can be changed back by the same program in case something went wrong.
http://home.t-online.de/home/thomas-rapp/killrdb.lhaWithout an RDB the HDD appears as empty. For your setup this means one LUN appears as empty. It could be repartitioned and reformatted.
BTW, you could also try to boot without startup-sequence, then quickly (before the disk-validator fails) do a quick format of the partition and then reboot. This is probably faster than all the effort of unmounting and wiping the HDD. You can also get back the data with DiskSalv.
Bye,
Thomas