Is there a difference in a spartan and elite in Halo 3 MP?

No, the hitboxes are the same for both. However, the neck of the elite is rumoured to be immune to damage except from a charged plasma pistol shot.

In Halo 3, the neck of an Elite (regardless what Armor Permutation used) is completely immune to any form of damage except for a shot from a charged Plasma Pistol. In addition, the projectile will simply pass through the neck, as though the neck wasn't there, without a blood spatter. This is because both Elites and Spartans share the same hitbox (where you can hit the character), but have different models.

Source: Halo Wikia