1. that pulsed phasers, and to a lesser extent, torpedoes (photon, and quantum) cause "bleed through" damage to the targets hull. with pulsed phasers there is almost always atleast some bleed through damage to the ships hull even when shields read 100% powerlevel, and torpedoes start to get bleed through damage at about 60-70% (quantum torpedos have greater bleed through damage and a higher level of penetration). now, i have also noticed this with Starfleet Command: vol 3 (/w the TNG mega mod aka dominion wars+). will the mod have bleed through damage at some point? if not, that's cool. it would keep the battles longer if you did
I dont really know what u mean

2. when you add the dominion to fleet ops, will they have poleron (that can't be spelled right) beams, and torpedoes as primary weapons? and will the other races be able to develop shields that those weapons can't instantly penetrate?
It would be great that races would have to research a counter-measure for dominion weapons, though I doubt this will be the case. Simply because of at least 3 factors:
first is balancing, just think if a dominion player would choose to rush at the beginning and noone would be able to hold them
second is simply because we dont know what about borg or noxter or ciadan or iconian

third is that I dont think this can be done

watching the movies/tv shows i noticed that damage to the warpcore can and most likely will cause a warpcore breach, and a destructive shockwave follows shortly after. is this going to go into the mod at some point if it is possible to create a script or something that can measure warpcore damage, or something like that and trigger a breach? keep in mind that it wouldn't happen every single time, but once in a while? like by %ages or something?
That would be great and then ships would cause some serious area damage

but it would only happen to like 1 in 20?? Also it would be great if this was somehow linked to the engine system, so when it gets destroyed or something it might also cause a warpcore breach