1) Yes, doing a NAND restore replaces the entire flash chip with the contents of the NAND backup file. This includes the diagnostic menus (at least it did on the C760/C860 NAND), the kernel and the NAND flash partitions.
2) Nope, flash rom is a jffs2 (or possible other filesystem in the early zaurus) image that is written to the read-only portion of the flash chip - not sure of the C3000 partition layout, but I think it holds true. The NAND file is a snapshot (with error correction data) of the entire flash chip. It includes everything!
3) As I don't have a C3k I'm only guessing here, but from looking at the ROM image from sharp, it contains a jffs2 image that is written to the flash chip and a tarball that contains data for one of the partitions of the microdrive. I assume that anything with the same name will be overwritten, but other data that doesn't exist in the tarball would remain after flashing.
4) "reset" on the C760 and C1K deletes all data on the read-write partition of the flash chip and recopies the original data - I assume that the same is true for the C3K but that it also deletes data on the microdrive (note: again I can't say for sure as I don't have a C3K)
5) A kernel is not a NAND or a ROM, although the NAND backup contains a kernel and everything else on the flash chip. It is possible to flash a kernel without updating the ROM as well as update the ROM without updating the kernel.
6) NAND stands for NOT NAND, and is a type of logic gate. http://www.nist.gov/dads/HTML/nand.html
. You can also get NOR flash chips too.