I'd like to add, that the Breen weapon might be a progression to a prior existing technology.
The Breen might not have been able to refine their technology until they teamed up with the Dominion. The first model might have been of a more supportive nature to pirate operations - perhaps to cripple some of the secondary energy systems to gain access to the ships transporters ...
Starfleet Security Systems(TM)("To your polished new Starship we might even add a fith failure safety.") might have been to advanced to effectively have been sobotaged by the first model. Thus, Starfleet Intelligence didn't care much.
...till the Dominion came.
But, with all we know, Starfleet Intelligence might have undertaken investigation in all the known cases. Just off-screen.