Awww, such a cute little fluffball :inlove: You must be loving every second of this. Babies are so much fun.
She's fine not staying in the nest anymore. Pretty impossible at this age to keep her in anymore. You can just go ahead and remove it if it is still the nest with fur and stuff. It looks like she prefers snuggling with mom anyways. The only thing to watch would be if she is small enough to fit through the bars of the cage. You don't want her getting stuck. Could zip tie some cardboard pieces along the lower edge if that's the case, to prevent any accidents.
You want to wait til the baby is weaned to get the mom spayed. Then if you still keep them together after, just watch that mom still accepts the baby being around.