I’d tend to agree with you, Josh. Unless the answer is that females are 100 times more frail than males then I can think of a dozen better reasons than “98% of the fish are males”.
So, I thought perhaps the same thing was going on with Sawbwa rasboras. You tend to get 98% males with those, too. And, like the Dario, they're a tiny little fish that no one in their right mind is going to go through and filter females. I never saw how it is worthwhile -- especially when you consider that you're likely seining a bunch of these guys. Given their stronger sexual dichromatism and dimorphism, it's certainly possible that you get a seine full, and "that's one, that's one, that's a female, toss it back, that's one, female, female, toss, toss, that's a dragonfly nymph, etc."
But, in this case, it turns out there's something really nefarious going on. When you put 500 of these guys in a big trough, waiting shipment to the exporter, or when they're in that bare tank at the wholesaler, they act a lot differently than what you'll see in your home tank (or maybe not that differently). We think of some of these fish like this as "schooling" fish, but they're not. Instead, juveniles and females school, while males shoal, usually setting up territories and harassing females. When they're pushed into tight quarters, the males respond to all the other males around them by dialing their hormones up to 11. They get super colourful, and they get super...
Hey, who is in charge of banning people from the forum? Whoever it is, don't read this post, okay?
They get super enthusiastic and, I'm going to use the word "randy". They immediately go from "Hey, sweetheart, how about you and I duck into the cabomba?" to acting like a 1970s construction crew. And there's nowhere for the females to seek respite.
So, you have a trough with 500 of them in there, and you lose 100 of them going to the exporter, and the you lose another 100 on the way to wholesaler, and you lose another 50 on the way to the retailer... and virtually all 250 of those are females.
And, somewhere early in that chain, they figure this out -- probably at the initial holding facility, which is buying from the collectors. They're not dumb, they tell the collectors, "I'm not paying you for the ugly ones that always die, just toss those back."
And, wham, there's your incentive to collect only males, which only exacerbates the problems for whatever females slip through (now instead of 250 males harassing 250 females, you have a tank with 450 males and 50 females -- those females definitely don't last).
So, while this is probably not applicable to female scarlet badis, it could be a component. Store populations may be male heavy, regardless of selection by the collectors / breeders / etc. because the females experience higher attrition along the chain.