Atlases made from orbiter photos do have the problem Matthew mentions. The Clementine Atlas is the newest example of this. Because of it's orbital perspective, it is seldom recommended as a scope-side atlas, but rather as a research tool.
There are a number of photographic atlases using earth-based photos and perspective that try to solve this problem.
Drawn maps have the advantage of being able to show single angle of libration and a single angle of illumination for the entire surface of the moon at the same time. Many drawn maps can also depict fine details that are less obvious in even the best photos (basically, some lunar features just don't photograph easily). All this aids in identifying features.
Many photogrphic atlases, like the popular Hatfield atlas, use a number of photographic plates of each section of the moon showing different librations and illuminations in order to achieve the same level of certainty for identifications. This has the advantage of showing a view quite close to what is seen in the eyepiece, but may still leave some guesswork on the part of the obsrever.
Oddly enough, the very best drawn maps of the moon do their job well because they represent an unnatural, physically impossible view of the moon. The best photographic atlases do their job by offering many views of the moon, all of which are quite natural and perfectly possible. Orbital atlases depict the greatest detail of all, but from a perspective impossible for the observer to achieve.
There are even combination atlases that use photgraphs that are air-brushed to simulate a fixed angle of illumination for the entire surface. The maps used in LunarMap Pro software use this method, and I believe the Virtual Moon Atlas does as well, though I'm not 100% sure.
In years past, I've gotten into the argument of which is best. One friend suggested that the 'serious' student of the moon should only use photographic atlases. I countered with the point that 'serious' students of any subject use all the resources at their command. I don't know if I was right, but it sure shut him up!