If mom wasn't caring for them then they did need to be removed and cared for.
The biggest issue is behavior. From 5-8 weeks puppies are usually learning proper manners and behavior from mom/littermates. A lot of pups taken before 8 weeks, for this reason, have behavioral issues. If you had to take them away from the mom, it would have been best to take ALL the pups in the litter until 8 weeks.
Since I'm not a breeder, I can't say if there are any health impacts.
Mom To~ Dakoda (b/t GSD), Simi (b/w DSH), Nashoba (sable GSD)