@Nervoussubject,
I can't tell you for sure but I suspect the other children will also be pulled from the home.
Will HUD be notified? I don't know but it wouldn't surprise me if they were told your sister and BIL were harboring people hiding from CPS, and that the rooms are in a filthy condition. Roaches, rats, bedbugs are all a very real problem with dirt and they could spread to other apartments. Stacks of dirty clothes are tripping hazards (at best) and stacks of other junk could be fire hazards.
Is there any way for you to temporarily take the kids into your (presumably) much cleaner home? That wouldn't necessarily change the outcome for anyone, but your nieces would at least be with family.
PS Contact Legal Aid and get a lawyer. Your sister and her family will need one, and you'll need one if you want to intervene on behalf of the children. Please don't try to navigate something like this without a legal professional on your side.