I had this come up earlier this summer. Two organizations wanted to have the same course measured for races about six months apart on the annual calendar. I tried to explain to them that one certificate would be OK for both events, but they wanted certificates for both events. So I measured the course, drew two copies of the same map, prepared two certificates- one with the name of each event- and charged them an extra certifier's fee.
I had the same question come up a couple of years ago on a different course but the two organizations agreed to give the course a generic name and only one certificate was issued.
The posting of the certificates to the USATF website turns the course map on the back of the certificate into a bit of a marketing instrument and I can understand why race directors want a course map with the name of their event posted on the website as opposed to one with only a nine character course certification code.
Given that I've certified around 400 courses over the past three years and this has come up twice, unless other certifiers' experinces are different than mine I don't think we have a major issue here. I'd almost rather issue redundant certificates than field the "can we use somebody else's certified course?" calls.