@pilot00: I'm not sure what you mean by "classed as a military vessel"? I have downed UFOs with those. In fact, currently I have the Bonny with 50mm + Charger laser and a hunter killer with 30mm + 25mm. The hunter killer can down large scouts by itself.
I have used both together to take out some more shooty stuff. Usually use the bonny to go first, soak up some damage, disengage at ~50% and let the hunter-killer finish the job. It's a risky thing to do though and a streak of hits can lead to disaster. Losing the bonny, the gals and their equipment is not something you can really recover from. But what's pirate life without some risks?
I am now making stingrays for the hunter-killer. I am also about to start building another interceptor, can't remember which though (either heavy or improved.. I got them at the same time and I can't tell them apart from memory), which will get rockets or cannons, or whatever the tech I am researching now turns out to be if that's better than what I have. I'll eventually make another 50mm for the Bonny, to take out small crafts, but it will increasingly be a transport since risking the gals is not a good thing to do.
@Galwail: 15 brainers indeed seems like enough until later in the game. They are not cheap and sustaining them depends on getting valuable shipping. I've been lucky with freighters one month, and now shrine ships, but on months where all you get are raiders or gunships, it's can be hard to cover their cost.
Panzerfaust are too expensive for my taste. High explosive packs do the job fine (I've blown up both cyberdiscs and humanist tanks with HE packs, boomosaurus and reapers are even easier), dynamite is almost as good as a HE pack and cheaper. RPGs are decent and you can loot some and make your own after some research too.
Otherwise, I've had a fair amount of luck with flamethrowers too, and sniper rifles are handy (especially with plastasteel ammo). I used to use the boarding gun as a high powered support rifle. Submachine guns (for reaction and accuracy training, and damage once you get acid clips) are good, confederate eagle and magnum (acid clips) work well with some higher accuracy troopers, and BlackMarch SMGs are not bad. Oh, and dart rifles with stun clips you loot, to grab some unarmored targets that are just far enough away you can't melee them.