Plugging in headphones used to be the quick and dirty way to assure silence (back in the PPC hardware days).
Now, the self test startup chime still uses the internal speaker whether or not the headphone jack is in use, but the below trick will work on older macs. It is of use with new macs as long as you don't set your mac to reboot automatically and you don't forget about the current behavior and reboot it yourself.
I have a snipped nub of a headphone jack that I use when I am in a place where noise is prohibited no matter what the software decides.
You can get a plug without any cord for less than $5 at a store such as Radio Shack if you don't have headphones you can sacrifice or the cut cord doesn't please you.
It's simply not possible to change the NVRAM mute/volume setting after the mac is shut down (or sleeping) so even if you prepare properly, sound will be made if things don't go as planned on the shutdown.