...and doing an additional sprite layer for every single ship would be a bit of a pain. We handle friend vs foe identification through symbolic overlays now, as y'all of course know.
I don't really see why it would be
that much of a pain. Sure, it would take a little time to paint up the alpha channels on the sprites, but assuming you leave out fighters (where color changes wouldn't be very noticeable), you'd only have about 35 ships to edit. And as for friend vs foe identification, I figure that this customization option would really only be used by the player, and maybe minor factions. It would be purely visual fluff, not something used to determine who your enemy is.
Not saying you should spend time on it though--honestly I really don't care either way. But this would probably be the easiest to implement of all ship customization suggestions I've seen so far, as badges/flags/decals would require you to make room for them on each sprite, as well as ship names.