hmm. it doesn't seem to be that there are missing textures, but rather some hi-res textures were not used within doom, mainly the wall textures.
for example, in Doom 1, the first level. go through the first door, and on the ceiling you'll see computer displays. it's still the original doom textures, and yet i do have planet1.png in the doom1 folder of the pk3 file located in Doom/vavoom/basev/doom (which contains basepak.pk3, flats.pk3, and xwalls.pk3)