Can't speak for all the historic Italian figures, but Leonardo da Vinci was referred to this way, because he was the illegitimate child of a notary and thus he could not bear the surname of his father. Saint Francis of Assisi was probably named so, because he famously renounced his father's legacy and wealth upon converting. In fact, his real name was Giovanni di Pietro Bernardone, Pietro Bernardone being his father, and was nicknamed Francesco, or little frenchman, because his mother came from Provence and he was fluent in Occitan.