Even if the change went the other way, items that used to be unlimited and become unique don't get taken away from players. I've still got several extra ophidian canes, triolic pattern enhancers, and subspace field modulators, which were all made unique. My away team still uses them just as well as they did before (which is really badly, but that's another discussion).
But.... wait, aren't BOffs already restricted to only being able to equip one weapon?
But your captain isn't. Basically, what the change is doing is letting you get extra guns for your boffs without letting you equip two of them on your captain. Before the change, you can only get one, period.
They could. I'm betting the current tech just counts how many of a set you have though.
I'm pretty sure it counts only what you have equipped, and only if the pieces are all the same rank.
With a Klingon character of mine, while I was collecting the Breen set, I had just finished getting the engines at RAUH, and then dinged to VA before getting the shields. So when I took the mission that rewarded them, they were at a different rank than the engines. As such, they didn't "count" for purposes of collecting the whole set (which surprised me a bit). Had to go back and redo that mission in order to get the matching ranked engines.