if you mean the main icons (tools, users, music, video) etc, they don't seem to be inside any RCO and I've yet to find where they are.
there is an RCO file with these icons inside (forgot which one it was) but changing htem only changes the icons for INGAME xmb, not the normal one.

there's several possibilities...

1) they are inside an SPRX file (i looked at few of them but havent found graphics inside of any so far)
2) they are in VSH(main).rco which is not present on the flash0 that is visible to us.

i have found references to a pile of rco and sprx files that are not present in the flash0 from the bootloader and I've yet to figure out where they are.
..however, i also found a string from the bootloader that calls a partition called dev_SYSTEM which no one seems to know what it is....

there's still a lot of work to do before proper 100% flash0 themes can be done :/