The end point will still be there, just not visible in the joint editor. The same will be the case for any body part that has a child. You are correct in that adding children will affect the head end point which could upset conforming.

Suggest that once you have added all the required children that you use the Wardrobe Wizard Copy Joint Parameters tool to copy back in the original head start and end point centers.

Wardrobe Wizard > Utilities> Figure > More > Copy Joint Parameters