First, It depends on your cat honestly. If she is aggressive towards people handling her young, you may need to leave them be, otherwise some felines will reject their young if too tramatized and they end up starving to death. If she seems okay with you touching them then she may be okay with them being moved if it is to a comfortable location (usually dark cave like boxed in areas such as a closet with a large box or designate a bathroom and a shower with lots of blankets) cats like to feel safe and like their young to feel safe so the more enclosed and away from noise or things that may disturb her, the better.
Second: Yes they go to the loo but the mother has to stimulate them and she (sounds grose) eats it. Sorry grose but true.