You most definitely can and rightfully should!
pk3's are basically a transparent solution for running updated code on top of the 'data pack', called something like data20080511.pk3.
Consider the Nexuiz data directory (~/.nexuiz/data on OSX/Linux || /Nexuiz/data on Windows) the root of your package and creative a zip archive relative to this.
You want to update files in the gfx folder, so your package would have to have a gfx folder inside it with the files you're updating. Rename the zip to .pk3, drop it in your Nexuiz data directory and it should load when Nexuiz starts.
I go into a little more depth on this topic
here if you need.