Being able to use an external drive as the NAND memory provides peace of mind knowing your Wii will still be okay and your hax can be backed up no matter how badly you muck around with it.
I'm no expert on hacking the DS, but from a programmer's perspective, wouldn't it be possible to include some sort of random element in the patching process (by way of random junk code, etc) to mask the patching algorithm at every launch?