but draining anti matter is only temp and you do loss the ship
its note like the antimater wont be restored in a few minutes
Eh, draining a key enemy's ability to use antimatter powers just before a fight can pretty much guarantee a win. Try removing, say, an Advent Mothership's AM and that Advent fleet isn't anywhere near as hard to take down as usual without the mothership to replentish the Guardians shields. (take the Guardians AM away as well and the fleet'll be mincemeat in moments compared to yours)
In other words: yes, the AM will be back in a couple of minutes, but that only counts if they live that long.