Manifolds are much cheaper to make than headers, that's why most cars leave the factory that way, good headers are often a cheap and easy way to improve a cars performance - both power & economy. Certainly that was the case when I first took an interest in engine tuning on the little 4 pot engines in British cars of the '70s. Any tuning guide recommended upgrading the exhaust as a first step, some engines responded better than others, minis would typically see an increase of 10 bhp from a manifold change -from 38 to 48 bhp - enough to power a th400!
Most people who fit headers like their car to be a bit louder, since the rest of the exhaust system often needs to be modified or replaced it's a good time to fit one that gives the desired sound.
I prefer my car to be as near silent as I can get it, headers can work well with this, a good exhaust fabricator can make a quiet system with little or no performance restrictions. The downside is it will cost more, mufflers are more expensive than straight pipes, particularly good ones.