They meant for there to be no horse armor for S-horses because it is rare. The chances you'll find a S-horse or have a horse struck by lightning is 1.5–4%. Factor in the chances for a thunder storm, which is a 1.44% chance. That means there is a 1.44% chance for there being a 1.5-4% chance of there being a S-horse. That's a 0.000324% chance you'll ever see one!. They didn't intend for there to be horse armor for them because Mojang thought it wouldn't be necessary. And because they aren't really used all that much, they also thought it wouldn't be necessary as well.