Down side is fletch clearance is harder with small shafts as is putting a helical/offset on them and long fletchs.
I think that fletch clearence would actually be better with a small diameter, wouldn't it, or do you mean through a prong rest, then I would agree that if you use a helical on the arrow, you may runinto issues.
I've heard people mention the difficulties with putting on a helical with smaller shafts, but I have not found this to be a problem at all. But maybe you mean the extremes. I have alway had an easier time getting a helical on 22-- then 2613 aluminums, and even most carbon shafts. I have never really tied any of the extremely small shafts though. This would be on a Bitz jig.