Would SF use these weapons against the Dominion, or Romulans in a desperate situation? Who controls these weapons SF Intelligence?
I would suspect Starfleet would use whatever weapons were able to cope with whatever desperate situation existed, whether from a rebuilt Dominion (unlikely since Odo's assured them the Federation is okay), Romulans, or even some alien race we've never ever heard of. For those one-shot Borg Busters they might hold off as they could be excessive firepower depending on the enemy. Sorry to admit that I misinterpreted the abbreviation in the "Future Dom War" title of this thread as meaning something completely different.
That VOY super-tech was probably thrown into the warehouse where they also keep the phasing cloak and the ark of the covenant.