One reason is that it would be like hanging a picture using a sledgehammer. If you're just studying various ways of unwrapping a sphere, the (very deep) theory of manifolds is not necessary. I'm not a cartographer but I would assume they care mostly about how space is distorted in the projection, and have developed appropriate ways of dealing with that already.

Another is that when working with manifolds, you usually don't get a set of global coordinates. Manifolds are defined by various local coordinate charts. A smooth manifold just means that you can change coordinates in a smooth (differentiable) way, but that doesn't mean two people on opposite sides of the manifold will agree on their coordinate system. On a sphere or circle, you can get an "almost global" coordinate system by removing the line or point where the coordinates would be ambiguous.

I'm not very well versed in the history, but the study of cartography certainly predates the modern idea of an abstract manifold. In fact, the modern view was born in an effort to unify a lot of classical ideas from the study of calculus on spheres etc.