Named Unique Auras do NOT stack. However the Aura Article specifically says that the Captain Enchantment is a passive effect and NOT an Aura.
The following is an example of a traditional "Aura"
Text is copied from Preseason Item Page and can be found by expanding the Runic Bulwark item.
Runic Bulwark Cost: 3200 (650)
+30 Magic Resist
UNIQUE Aura - Legion: Nearby allies gain 10 Armor, 30 Magic Resist and
10 Health Regen per 5.
(Unique Auras with the same name don't stack.)
The way Auras work is HAVING the item gives you the bonus and then you can get the AURA bonus from a nearby ally. (Having 2 Runic Bulwark on a team gives both of the holders the Aura effect twice but each of their teammates receive only 1 instance of the Aura). Having the Captain Enchantment on your boots and then an ally having Captain on their boots won't give either one of the champions 2 Captain Bonuses since the bonus only applies to allied champions moving toward the holder.
The question boils down to: "If those 2 champions stand next to each other, will a third nearby allied champion get 2 instances of Captain MS buff?" and if the Captain Buff is an AURA the answer is no because you can't get two of the same named AURA from allies.
However, according to the Aura Article the Captain Enchantment is a considered a passive effect and NOT an aura. Therefore, it would seem that a champion could receive a 16% ms buff if two teammates have the Captain Enchantment.