Walt From a lore perspective, I feel like cannon shells should be the most impervious to flak, though I realize that's problematic from a balance perspective.
I assume you mean "most" out of laser-missile-cannon, but still more vulnerable than ions or railguns?
I think it's ok for cannon shells to be more durable than lasers and especially missiles, as long as they're not nigh-unkillable. And since flak is AOE, it'll naturally be worse vs the slower-firing cannons anyway. Mostly I'm worried about current flak being nearly useless vs cannons, and being all-or-nothing (either you push the shell away or it deals full damage). I think it might make sense to just give cannon shells HP, and reduce their damage proportionally to the amount of HP remaining.
Would proportional HP/damage work for railgun bullets as well? I don't think flak will ever be shooting down a whole railgun bullet (and if it does that's a problem), but proportional damage lets flak be not completely useless vs railguns, without being very effective at all.
What do you think about making EB even lower hp? Since it deals very little direct damage, it seems like it would also be very easy to dissipate.
How do you envision flak vs ions? Is it feasible to have flak clouds attenuate ion beams partially - enough to make flak v ions not completely useless, but not so much that it's strong?
Walt The only thing that's slightly weird is, why is flak so much faster than cannons and lasers?
I think the real question is - why are lasers so much slower than flak?

Ok but jokes aside, I don't think this would be a big issue. Both ion beams and railguns already move faster than lasers, and fast enough ships can outfly them. Personally, I've always imagined lasers as "plasma blasts" or similar, since they definitely move slower than the speed of light.
And regular cannons shoot big, heavy, metal cannonballs, which probably take a ton of energy to shoot. Flak shells are probably very small and lightweight, so could the same amount of energy that shoots a cannonball slowly shoot a flak shell very quickly?
Walt What do you think is the most important part of the mine's magnetic attraction? Is it that mines are less attracted to smaller ships? In that case, what if mines weren't magnetic but were homing and activated by a proximity/movement sensor that is more easily activated by closer, larger, faster-moving ships?
I think the biggest part of attraction is making mines useable in direct combat. So I could get near an enemy, start shooting mines (either forward or out my sides), and they would hit the enemy instead of floating uselessly away. Attraction for pre-layed minefields is probably a lot less important (though still very interesting).
I'll probably agree with whatever mechanic you think can accomplish this. A proximity sensor sounds reasonable.