It's pretty fair to say that the vast majority shoots I've done end up with images where there are dark circles under the eyes.

Is it a rare thing that these don't need to be cleaned up in the retouching process (or am I doing something wrong in prep - either MU or lighting/camera work)?

Do you have any images in particular that demonstrate what you are experiencing? It could be a case that lighting could be improved on set or it could be that a lot of people just have dark bags that need retouching

It a combo of a lot of things. Maybe the lighting if you are shooting for beauty it is a lot less for editorial more, etc., etc. but usually there is something there as it should be. Some clients want it taken down others removed. I have worked with really great images w top notch photographers/makeup/stylists and there was still eye bags there just do the best you can do. It's a good thing you are thinking this far down the road it only makes you an asset, just don't leave clumps of make on the face. : )

A couple of slices of cucumber  for the talent to place on her/his eyes, while you get your gear set up.

Often times if there are really dark circles it may be your lighting, adding a reflector or another light source directly underneath and in front of your subject aimed up should clear up the dark part of that problem. It also could be just the model and they have darker bags under their eyes before the shoot. The light will help either way though for sure. For beauty I constantly go back and forth using a reflector bouncing the octabox light back up into my subject.

Thanks everyone for the advice - it sounds like some darkness under the eye is normal, and it's not unusual for a little D&B there.