In a Civil War context at least, the problem is usually less a case of photos not existing than it is of photos being unidentified.
As today, people tended to take photographs for their own use or that of a loved one, and hence rarely took the time to mark down what the subject was. (They didn't NEED to; they knew who it was.)
For every identified photograph of a Civil War soldier, there are 20, 50, 100 more in repositories and private collections for which there is no positive identification. (As anyone who has ever visited the image collection at Carlisle Barracks can attest.)
Chances are that more than one photo of your relative exists -- it's just that we have no way of knowing that it IS your relative. And unless you were somehow to stumble across one someday and recognize it as such, we never will.
I'm not sure how you fix that problem. Maybe with some giant metasite where everyone scans in whatever unidentified Civil War photos they have, and everyone else in the world can look at them. Law of averages, would suggest that some of them at least would get recognized. (A Wikipedia approach to the problem.) Or perhaps someday one could manage a technological fix to part of the problem: scan in all id'd photos and all the unknowns, and let recognition software try to make matches. Admittedly, that would only help for soldiers of whom at least one identified photograph already existed, but I bet it would cut through a fair chunk of the backlog.
I'm having that problem know with a collection of letters I'm editing from a Lt. in the 12th Va. I know there are at least three seperate wartime images that were made of him, because I have the letters where he talks about sending his photos.
No one in the family appears to have the pictures anymore. The letters were donated long ago to a repository. Chances are that the photographs -- or at least one of them -- is also in a collection somewhere, unlabeled.
It's hard to believe that 100 of his letters and a wartime diary all lasted for 150 years, but that none of the three photos sent to three different people did.
The joys of our field. But it still beats modern history. ;)