After you've decided on hubs, rims and pattern, your source for spokes should be able to determine the spoke length you require. If not, try to find Sutherland's Handbook for Bicycle Mechanics. It's just that small-flange hubs do the job well enough, and the amount of extra strength afforded by large flanges isn't worth their extra weight. One conspicuous exception is track racing, where large-flange hubs are still practical and popular. When choosing among small-flange hubs, weight is a relatively minor factor because most models are of similar size and their mass is concentrated close to the wheel's rotating center.
Wind resistance is also a minor consideration.
An aerodynamic shape is worth a lot more in looks than performance. As a rule of thumb, choose hubs that cost the same or a little less than the pair of rims you've selected. Cheap hubs may give good service, but only for a couple of years. Then add the same amount of spacing between the left-side cone and locknut. Have your local shop spread your rear triangle to 126 mm, if necessary.