Arcane Propulsion Armor can give additional body parts to the wearer instead of "missing" ones:
If the wearer is missing any limbs, the armor replaces those limbs—hands, arms, feet, legs, or similar appendages. The replacements function identically to the body parts they replace.
An artificer provides such an armor to a naga. Naga has no legs, so it is missing them. Will it get legs from the armor?
In this particular case "missing" means that you do not have something any more. This interpretation is supported by the other verb in the description (emphasis mine):
If the wearer is missing any limbs, the armor replaces those limbs—hands, arms, feet, legs, or similar appendages. The replacements function identically to the body parts they replace.
Replace means to take the place of something that was there before: hence, if you had a leg and you lost it during a fight against a Kraken, then Arcane Propulsion Armor can replace it with a new one. But since a Naga, as in your example, never had a leg the Arcane Propulsion Armor can not replace it
