Because Samurai wasn't actually poorly designed for what they were supposed to do originally. The reason Samurai never really caught on as a tank was because Parry was so difficult to level up. Without nearly capped Parry, Samurai couldn't tank better than pretty much any other melee class subbing Warrior. In addition, anyone that didn't actually know Samurai was supposed to be a parry tank would just assume they were a DD due to their weapon selection, armor options, and abilities. The AF is probably the first clue most people had they were intended to be a tank and by then, they had been playing them as DD for a long time.
Ninja, on the other hand, couldn't do their job effectively. Their damage, especially back then, was pretty lousy for a class intended as a DD. Their debuffs were also pretty pathetic due to how difficult Ninjutsu was to level up. Even if you had Ninjutsu capped, the only unique debuffs Ninja has are the elemental ones, which just aren't good enough to build your entire class on. So a DD with enfeebling did lackluster damage and most of their debuffs are castable by multiple jobs. However, Utsusemi, which was just intended as a safety net ability made them nearly invincible in some situations when used properly.