What are you searching for? SSH is just the method of accessing the Pogoplug's underlying Linux system, so a search for "SSH commands" won't yield much. You likely want "Linux terminal commands" or "Busybox commands"

Anyway, as for the commands you need:

List devices/list disks: "cat /proc/partitions" should show all storage partitions, even unmounted ones. Won't show other devices though
Recognise hard drives no matter where they are: type "blkid" with the drives attached, you should get output like this:

/dev/sda1: LABEL="OPT" UUID="7601b7f8-60e6-4662-8d3e-3e5860ee8cfd" TYPE="ext2"

/dev/sdb1: LABEL="M-^IPNG^M^J^Z^J" UUID="64C9-30D5" TYPE="vfat"

the UUIDs are the Unique ID numbers for those drives. replace the /dev/sda and /dev/sdb parts of your commands with those IDs and they should always affect those drives no matter where they end up in the device list

that Should work with hdparm. I know you can mount by UUID, so I don't see why not. worth a shot

set Samba share name: not entirely sure what you're talking about here, whether it's the hostname or the share name itself. run the hostname command and if that's showing FADSxxxxx. then you can just run hostname newname to change the host name. if it's the share name itself you want to change, locate and edit your smb.conf file, seatch for FADSxxxxx and you should be able to change the name. Cack up your smb.conf first though!

HDD permissions on startup: not entirely sure about this. Normally the startup mount settings would be in fstab, but pogo doesn't have many entries in there. you could try setting their permissions in the rcS file, but I don't recall seeing the USB drive mounting config in there.

Hope that helped,

Stefan