Yup. Except for the purpose of determining what you can hit. And by that, I mean that if you're fighting an enemy that requires magical weapons to hit, you'll need to have magic ammo; having a magic launcher is not enough.
As TJHooker was saying, only the plus of the ammo matters for determining WHAT you can hit. If a +2 weapon is needed, you must have +2 ammo. But launcher and ammo pluses all stack for hit and damage rolls.
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