A LUN is a logical unit inside the physical device. Each SCSI device can have one or more LUNs. For example a 6-way CD changer has 6 LUNs, one for each CD slot. Whenever you access one of the LUNs, the changer will move the CD from the respective slot into the CD drive so that you can read it.
In AmigaOS the LUN is usually specified in the tens place of the unit number. So if your device has SCSI ID 2, LUN 0 is unit 2, LUN 1 is unit 12, LUN 2 is unit 22 and so on.
HDToolbox actually does not know about LUNs, it just scans the unit numbers in a specific order.