What would you do if your son in mostly honors classes got 2 D's?

Yay, I think that's too much, I don't think punishment would do good. Besides what he did isn't a crime, everyone has there own downfalls, punishing him will lead him to have resentment for you. Rather, just give him encouragement and incentive if he's able to pull those grades up for the next time. and do appreciate his mark on other subjects then he'll surely look for that appreciation for those 2 subjects thus motivating him to do better to those two subjects.