There is a discussion on fiddle-l on this very topic, back in March/April of 1998; you might want to look it up in the archives; otherwise, I'll provide a link later on if I get the time. Based on what I read there, which was rather inconclusive ("more research needed"), and what I've picked up about other traditions in other places, I suspect that it had to do with fashion in dance: dances in 6/8 time went out of style as some new dances in 4/4 became hip, until the 6/8 repertoire was largely forgotten (although one or two contributors to the fiddle-l discussion recalled one or two specific old tyme Southern fiddlers who had a number of jigs in their brainbox). By the way, in that fiddle-l discussion, it was stated that the lack of jigs is a feature of southern as opposed to northern (New England) fiddling.

Back to dance. Somewhat conversely, in the Cape Breton tradition there is a vast number of jigs - but these were not "indigenous"; they were adapted from the Irish or composed to accomodate changes in popular dance forms in the early 20th century.