I think the nidhoggr applies the full damage to shields even after it's done some damage to the hull. I think the easiest ship to test it on would be a fleeing dominator. It has a (relatively) small flux pool so it's be easier to visually gauge the amount of damage to the shield. That's how it feels any way.
I like the new things added since i last played (4.4). My favorite thing is the splinter pod. It's everything i wished the annihilator pod was plus emp damage. I really like the small polarizer. It's like a strike emp weapon. I haven't found a role for the large polarizer yet, but I haven't had large enough fleet to really specialize either. Is there supposed to be a medium polarizer? If there is it hasn't been delivered anywhere yet. Also the assault beamer is surprisingly good against armor.
The southpaw is very strong. Like a faster brawler. I like that the two mount sizes are paired like they are. It makes aiming long range weapons (like HVD) much easier. Its small shield leaves a bit to be desired, but with tech skills it ends up being ok. Also the shield is blue.
I noticed the CR costs have risen pretty much across the entire spectrum of ships too. Probably for the best balance wise. Was the CR% recovered per day increased a similar amount? I can't recall what it was before. If it wasn't, it isn't a problem right now because everything is basically a pinata. I haven't tried the fighters at the new cost though. I just started increasing my FP total so i'll see how they do shortly.
I've been making it a point to only scavenge or to buy from the SHI station in anticipation of the next update. I've been making exceptions for the SHI ships/weapons i haven't found at the SHI station. This has led me to use the troop transport quite a bit. The 20% troop buff seems to work fine. What does the active ship system do though? I think it slows the enemy turret turn rate, but i'm not certain. I use lots of splinters and annihilators so PD (what i expect to be most affected) doesn't do well anyway.
I would like to request that the tanker requires 1 person. That way it can be a tiny bit more resilient and slightly faster in the event of a flee scenario. Any time i have to flee it dies horribly. It'd probably die horribly as an elite too, but take long enough i might be able to distract the enemy. With regular skill it'd at least be able to shoot down the first pilum of a salvo so it's flux doesn't spike so precariously high.
If i've missed any of the new stuff please let me know. I'd like try it all out.
EDIT: I've managed to try out the thresher. It has a lot of gun. The smallish fixed shield mean without extending it or making it omni you're going to get the tips of your wings clipped often. Its shield is also blue. I love how much missile you can cram on it though. It feels like flying a TuP ship because of the wide array of assorted mounts. The ship system is better for the AI than accelerated ammo feeder because after its filled its flux by firing swiftly it has to fire slower and lets the flux cool off a little (as opposed to AAF that just fills it and then the ai hovers near full flux until it or its target dies)