Re: Phaser arrays, it's not like slapping an onion ring on top of a beef patty. Everything under the ring has to be able to support the mass, volume, and energy requirements of the actual array. The older ships probably just didn't have the infrastructure to support the larger weapons, so they just improved the ones they DID have with the ability to fire continuous orange beams instead of pulsey pink ones or solid blue ones, or whatever. Up close, the older arrays are supposed to be basically spherical turrets with a single emission barrel that is swiveled around as needed. Given that such detail is rarely built into the models of the show, and basically impossible to view on TV anyway, it's easy enough to think that they replaced the swiveling turret with a bump that could fire in any direction in a 180-degree arc, without any need to physically traverse the array.
Re: Breen Beams, I'm sure that once they learned Starfleet had defeated the weapon's effectiveness, the Breen immediately started working on ways to distrupt the anti-disruptor. However, the war was over a matter of days or weeks after that, so it's pretty much a moot point. The Breen seem to have survived the war with very little lost compared to pretty much every other party in the conflict, so logistically I can see them continuing to tinker away on creating a better version, unless the victors imposed a ban on further development on such weapons (as well they should, and this sort of thing happens today).