I don't know how much things changed since I last played but your talk of baby nukes seems to indicate that the main thing didn't change. When I was farming them, it was church supply ships, which also means chryssalids
After the first few, you quickly realize what you're up against:
1 - A timer that prevents you from taking your time
2 - Baby nukes and gauss that means nobody is safe (at least nobody I had, my best armor being juggernaut and loader).
The timer means that you
have to scout rather aggressively, you can't afford to take your time and be careful. With the weapons they have (and chryssalids in my case), I found that using smoke wasn't great, because one enemy unit walking in on you in short range during their turn means a dead gal. Of course, one enemy seeing you from afar also may mean mass casualties from a baby nuke, so smoke should be good..
My solution was:
1 - Dogs and (hig TU/stam) rookies.
They're expendable, so you can use them aggressively as scout. One expanding circle from the Bonny, with good spacing between each others and between them and your 2nd line so a baby nuke hits only a few gals. They are the skirmishers who flush out the enemy. You can smoke them at the end of your turn, but you can't stay in smoke as you need to spot the enemy first and ideally from far away. It should work better now that there is longer vision range in the day. It could actually work
really well with night ops gear on the rookie scouts, to give you the differential advantage in vision range so you can spot/shoot first. Killing first is the best way to ensure not dying
2 - Heavy long range second line.
Bring gals with long range heavy weapons (HMG, advanced sniper rifles, rocket launchers, etc. Meridian/Eddie would probably say bows too but I dislike bows from a conceptual point). Having them in flying armor helps to get line of sight on whatever the skirmishers find. Make sure to have them well spread out and hugging cover. If not flying way in the back, wearing pretty heavy and fireproof armor. The 2nd line shouldn't get shot at, but that doesn't mean the enemy won't miss a skirmisher with a baby nuke which will then blow up in your 2nd line. Having the armor/cover to survive the edge of blast, and the spread that only one gal should get hit badly can turn a catastrophe into a setback. There is no place for riflemen midfielders as you have to spread out too much because of baby nukes and you want either scouts or heavy support.
3 - Fast boarding team with Psi and motion scanners.
The supply ship is a small ship, but because its crew has gauss weapons, it is not something to underestimate. It plays pretty much like the classical XCom:EU boarding actions: Reactions is not to be depended on, and since the death risk is pretty high, you don't want to risk a high reaction gal, so you scout/strike/retreat with scanners and psi to play through the walls. I say Reactions don't help defensively all that much here since the shot you might be reacting to may well be a kill shot and dead gals don't react. They are useful aggressively (to prevent enemies from reacting to you), but you can work around that with motion scanners and good movement and you don't want to risk good reactions gals. The best is motion scanners to find them, psi to mess up with them (save a gal who went too far, or better MC someone and scout with so they eat the reactions) and just a few (2-3) gals to kill them. I would generally suggest using "decent melee swabbies" in cheap high mobility armors for the boarding, as the stats don't matter so much (and neither does armor values) and you don't want to risk losing a great gal to one gauss shot. Advanced armors that make you less vulnerable to gauss would change that, of course, but even juggernaut was too unreliable and too precious for that for me. The most important is your ability to use motion scanners and good scouting, and your witch's abilities to MC the enemy.
4 - Bravery is good
Looting supply ships is a high risk mission and there likely will be casualties. You don't want that to start a panic chain that costs you everything.
So farming supply ships won't be without losses, but if you do things properly your losses should be cheap enough. Dogs and rookies skirmishers are easily replaced, and you've got parrots now! it doesn't matter if they die easily, everything dies in a hit here.. and lots of good scouting is invaluable for looting supply ships.
For bases.. I haven't done it yet. The only ones I've encountered where mercenaries (and I didn't want to risk that), church (chryssalids!!
) or traders. I was farming the church supplies and intending to do the same for the traders (free power armor parts!), so I never tried. It all depends on the gear they have. If it is plasma/energy based, you can have some really great armors built with forcefield tech (ie large % modifiers on laser/plasma damage) that will significantly reduce incoming damage. I remember base defenses got significantly less lethal once I had Mesh Armors. Here good use of corners to prevent multiple casualties to blaster fire replaces large spreading, and short range and melee weapons are to be privileged with the close quarter fighting instead of the long range heavy support of the supply ship farming.