Several of the races for the Westport (CT) Summer Series consist of variations of a course. When I originally measured them, Dave Reik, the CT certifier at the time, issued multi-numbered certs for each. Here's an example of the maps:
Westport 3/3.5/5
Westport 4/6
These are all local events, so record quality isn't a consideration. What's nice about the way we did it is the RD only has to have a blown-up laminated copy of 2 maps, rather than 5, to post at the site on race day. And, he's only got to file 2 pieces of paper at home.
My own gut feeling on the multi-course issue is to consider them on a case by case basis. Some, such as large marathon/half marathons, should probably have separate certs and maps for each; the Joe's Brak & Muffler 5/10k, probably not.