Page 62 of Fully Operational says, "These items are new weapons that can be mounted onto starships or vehicles. Note that they do not replace existing weapons, but are extra weapons added to offer more firepower or combat flexibility."

Look at the second sentence there and tell me: Does this mean that these weapons cannot be used for the "0 HP swap" with previously mounted weapons but can only be add-ons that always cost HP?

Can I really not swap out a proton torpedo launcher with an ion torpedo launcher without paying a HP (and, if I do that, I might as well leave the proton torpedo launcher in place too)?

That is strange. The other books that add new Weapons Systems simply lump them in with Attachments. I would say that based on the nature of the Fully Operational weapons, that the answer is, "No".

However, I think you should send your question to the Devs and see if you can get an official answer.

Cheers!