Guido - Except for the scenario where BAA won't accept a marathon time run on a half-marathon course run twice, no matter the configuration.
For shorter courses, it may be fine to issue one cert for the one-lap length. I don't see any potential issues with this, unless a record is set, and the certification is challenged. Two (or more) laps of a certified course is acceptable under USATF guidelines, so that should not be a problem. Can someone (the old record holder) challenge the USATF acceptance of a two-lap record? I think not.
But, if an event is advertising their course as a "qualifier" for another event, it may be in their interest to spend the extra $30 or $50 (so measurer gets some compensation for making the second map, with reference only to the longer course) on a certificate for the second course.
But, if we have a 5k course with mile splits marked, a 10k (two laps) will have to have additional splits identified. That is additional work for the measurer, and additional info on the map. Another reason to only mark km splits!