Had to go look at the new power calc first, now to answer your question. No, the Aux DHCs are not limited to one per ship. It only comes with one, but you can dismiss and reclaim as many times as you like to get more. However, they can only be mounted on a Vesta variant, not on any other ships, so they are limited another way.
I think the aux cannons are only 1/ship as a selling strategy, so many will buy the 3 pack (or even worse, buy all separately after seeing one only has one cannon), as they think they cant get more than one :S
its a smart move from cryptic tho