For fasteners that are designed to be countersunk, the measurement is made from the point on the head where the surface of the material is, to the end of the fastener. Carriage bolts are measured from directly under the head.
Eye Bolts are measured from under the eye. Hanger bolt length is measured from end to end.Hex bolts are measured from under the head to the tip of the bolt. Lag Bolts are measured from under the head. Machine screw measurement depends on the style of head it has. Pan Head or Round Head screws are measured from under the head.
Countersunk (Flat or Oval head) is measured overall. Countersunk screws (Flat or Oval head) are measured by overall length.