Are you or another player on the map using Tactical Team? That does cause a lot of beeping noise as it is redistributing shield strength to you or another players shields. It will still occur after an enemy ship is destroyed as the last few torpedoes or cannon bolts are hitting your shields.
seems to be related to HY torpedoes, notice it more in fleet actions and mirror event. tac team makes a distinct sound different from the beeping so that's not it. but when i look around there's usually 1 torp just sitting there pulsing in time with the beeps. noticed another bug with HY's too, that when they hit they sometimes don't vanish, just sit where they were.
that and HY's in mirror explode strangely for being quantums. effects look more like what a plasma-quantum hybrid might look like.