I haven't noticed a difference so far in health of babies that needed assisting vs ones that hatched well on their own. I've had some health issues from a few I've assisted and a few that hatched without any help. Most of my assisted babies turn out to be healthy though. I think shipping just really throws a wrench in the works overall.
Safety holes are pretty safe as long as you candle and carefully add them to the top of the air cell where you won't be hitting any blood vessels.
I also agree you did excellently with shipped eggs! Late quitters seem to be very common with shipped eggs unfortunately (I certainly have gotten my fair share).