My hammies had babies - a litter of 9. I can't put daddy near mommy because mommy screams at him so the 2 are in separate cages. The babies are 8 days old today. I cleaned the cage by cleaning around the nest but mommy stinks of pee and I'm concerned that the nest itself is unhygenic? When can they get a new nest? I'm also concerned that the mom (they're all dwarf hamsters) is looking really thin and her fur is wet all the time.

You typically want to wait until the hamsters are at least 12 days old before you begin handling them. At this time you can try removing them from the cage to give it a thorough cleaning, as it can get pretty stinky by this point

As for the mom's fur looking wet all the time, keep an eye on it. You want to make sure it's not diahhrea making the fur wet, as that would be a sure sign of wet-tail, something that needs a vet's attentian immediately.