I play with mines off, which maybe is my own downfall in that sense (but in some cases it's not really relevant like for example when you destroy a counter-attack post and 1000 MKIV bombers appear in a random system nowhere near the wormhole). Raiders don't even get bonuses against polycrystal, Space Planes get a small bonus (x4), but laser gatlings and tachyon microfighters actually get a pretty big bonus. Still, that's assuming I can even get my hands on those types of ships, and assuming that I do, that they will be able to stop a massive wave of MKIV/V bombers anyways. For me it's not a question of whether they can be killed, it's how much damage they are going to inflict before I stop them. They are ironically the hardest ship to kill (from my experience) and also the most capable of causing the player to lose.
The best way I've actually found to stop mass bombers so far is with mass Riot Control Starships that simply destroy their engines long enough to, eventually, kill them all off. Though I think it's a bit unreasonable to expect the player to always have a fleet of Riot Control Starships on every planet that is in danger of being attacked by bombers, it also forces them down a tech path that shouldn't be absolutely necessary.
However, I agree with you that in the hands of the AI, which have no "time limitations" in that sense, 1000 or more of them are extremely hard to deal with. By the way, Fortresses have a 0.01x modifier against polycrystal, so that is NOT an answer to bombers, in the least.