Yes, or William. There would be diminutives: Jonkin ( or Jenkin) or Johnny. Age distinction: Young John, or Jack, (short for John-cock) as opposed to Old John. Patronymics: John John-son, or John Richard-son. Place names: John At-wood. Descriptions: Little John. You can see some of the variety in Curiosities of Puritan Nomenclature .

For 18th c. America it can often be a challenge to a historian, the sameness of names... trying to figure out which William or Mary is being referred to , in a family with three generations of them living at the same time.