Oh that's awesome!! Heartening to see you have more than you thought!
Mine blend so well into the sand, and I've had a difficult time getting an accurate head count since they hatched even, I've pretty much given up counting until they get bigger! lol. I was taking each loss so hard, it's almost better not to know how many I have exactly. I feel like I lost a lot, since I thought I counted 12 or 13 on Tuesday, lost one on Wednesday, then could only count seven or eight yesterday. But that many bodies couldn't have vanished, I'd have found them if they'd died when cleaning. So I'm hoping that there's more than I thought, just hard to see in the sand and in a breeder box.
They seem to be a little bigger each day, so I'm just going to do the same, continue feeding, cleaning, keeping the water good, and as long as I see some babies wriggling around, I'm hoping for the best and that some of them make it at least.
As for whether it's bacterial/water etc, I think it would be impossible to tell without lab testing. We can't see what's going on internally, perhaps a decent chunk of them don't develop properly, and that part is out of our hands. I know that the one I lost Wednesday was smaller than the others, he just didn't seem to thrive as well as the bigger ones, despite plenty of food available.