It really depends on the model of the AS/400 but some disk drives are in the base unit with the processor and memory and others are found in an expansion cabinet. Most small AS/400 machines will have the disk drives in the front. You ned to pop off the front cover to see the drive bays.
Do not remove any drives while the machine is running, it will shut everything down immediately and you might not be able to get the machine to IPL after that.
You have to have the base OS running and you can from the main command line look at the disk drives with WRKDSKSTS. This will show you how many disk drives there are and their location.
To be able to scratch the disk (Reformat it so the data is unreadable) you need to IPL the machine to DST mode and through DST initialze the disk drives. This will be the method that IBM uses when they come in and package up a leased machine to go back to the leasing company.
Another way is to pull the disk drives out of the frame and mix them up in different slots. Because the data is scattered across all the disk drives in a particular ASP, the system will not be able to read the data and will error out when it tries to restart. This will force a reload from the CD or tape media. This is faster but if anyone who gets this machine where to try and move the disk drives around depending on how many drives you had, then they might be able to get at the data.
Initializing the disk is the safest and surest way but once you choose to initalize the disk, kiss your system goodbye.