Speaking with only mice experience here

how long to wait with mice?......ha ha....until the smell gets to be too much or a week and a half....which ever comes first

I figure rats would not be as bad since mice tend to be fairly common baby eaters..

Rodent mothers tend to keep their nests very very clean. So if you don't want to disturb them but you would like to 'tidy up'....go ahead after a day or so.

If I need to clean enclosures before the week is up, I usually do it by setting up another enclosure for the mom and babies....they just kinda 'transplant' the nest and babies all at once into the clean enclosure.