The firmware is both on the hd and part of the firmware is on the flash. Everytime you upgrade your zunes firmware eboot.bin and recovery.bin are sent to the flash and then nk,eboot, and recovery are also stored on the hd. Each time the zune boots up the firmware from the flash chip checks for signatures in the firmware files on the hd, if it finds them it runs, if not it tells you to reinstall the firmware (Changing even one byte in the firmware files deletes the signature).
A lot of people expect the zune to be hacked when games come out, but theres a 99% chance that will not happen. With the implementation of XNA on the zune the security will be even greater, and with what it is now it could mean no hacking for a long time.
Hope that cleared up a few questions.
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