Some of these may not be worth bothering with, but I figured I'd list them all here since I've got an easy tool for looking through and checking. (And, apologies in advance for my inconsistent capitalization of ship names.)
List one: Shields or ship bounds extend noticeably outside collision radius
- Sunder: as per my mention in the modding questions thread, just relisting it here for completeness
- Gemini: shield & collision radii are equal, but the shield center is notably offset.
- Defender
- module_bastion_pd1 & module_bastion_pd1_lowtech
- Picket
- Ravelin: while I don't recall if these are actually shielded, their bounds polygon actually extends past the collision radius. (As does their shield radius, by a much more significant margin.)
- remnant_armour3: bounds polygon extends past collision radius. (shield radius also equal to collision radius, though that probably doesn't matter.)
- remnant_shield1: though I think this module isn't actually used? Still, collisionRadius 90, shieldRadius 200.
- remnant_weapon_platform_2: shield radius larger than collision radius. Technically can't have a shield installed in vanilla, but I know of at least one mod where that doesn't remain true.
- Sentry
- Shrike: shield radius is slightly smaller than collision radius, but extends forwards several pixels past it.
List two: Ships that technically have issues, but may not be worth bothering to fix. If there's no specific note, assume the ship's shields extend exactly one pixel outside the collision radius.
ships
- Astral
- Claw
- Salvage Rig: a 1.4 pixel offset; shield radius = collision radius, shield center at 1,1
- Derelict Mothership: will never have shields, so the shield radius being a hair too big shouldn't matter. Also applies to some sub-modules:
- pod_engine_left
- pod_m_left
- pod_s_right
- Guardian
- Hammerhead: About 1.4 pixels offset; shield radius 120, collision radius 130, shield center is 11,1.
- Khopesh
- Longbow
- Lumen
- Lux
- Merlon: An unusual case of the shield being offset one pixel to the side. Do these even have shields? I don't recall.
- mining_drone
- module_armor1
- module_armor2 through 5: shield radius is significantly smaller than the ship's bounds. Probably not an issue as these should never have shields, though.
- module_blocker2, 2b, 2c: ~1.4 pixel offset
- module_decor_midline1
- module_hightech_armour
- module_hightech_attack: shield is notably offset to the rear; given the use of this particular module, this is probably not an issue worth bothering with even though the shield circle extends noticeably past the collision circle.
- module_hightech_decor
- module_hightech_hangar: shield circle significantly smaller than ship's bounds polygon.
- module_hightech_strut: shield radius greater than collision radius, and bounds polygon that technically extends past the collision radius too... but I'm pretty sure this one's set to not even collide with anything?
- Omen: would be on list three if the shield center was 11,0 instead of 11,1; so that's ~0.4 pixels offset.
- Ox: can you even put shields on one of these? And if so, why would you want to? Still, shield radius 55, collision radius 55, and shield center 1,0
- Paragon
- remnant_armor1, 2
- remnant_hangar1
- remnant_station1: shield radius larger than collision radius. Bounds are also a bit odd and don't really match the graphics. As this is a station core component, however, both of those issues are probably not worth addressing.
- remnant_weapon_platform3
- Shepherd
- station1: I'm going to guess that this one isn't actually used. There's a one-pixel offset on the shield, but more seriously the image centerpoint is pretty clearly not set correctly.
- station2 & 3: shield radius significantly smaller than bounds polygon. As a station core component, this is probably not a concern.
- station2_midline, & 3: bounds polygon extends past collision radius. Slightly more serious than shield circle issues, but may still not be worth addressing.
- talon: ~1.4 pixel offset
- thunder
- venture
- wasp
List three: Ships whose shield and collision radius are equal, but have no offset on the shield center (or whose shield center offset makes the shield exactly meet up with the collision radius). This goes against the suggested ship design guidelines, but (probably?) isn't an actual bug.
ships
- Bastillon
- Berserker
- Brawler
- Dominator - an example of shield forward offset being exactly equal to the difference between shield radius and collision radius.
- drone_assault
- drone_borer
- drone_pd_midline
- drone_sensor
- flare (though I don't think this ship is used?)
- flash
- gladius
- Lasher - like the Dominator, the shield circle exactly meets the collision circle to the front.
- Medusa
- Mercury - also has distinctly over-complicated bounds, though, given the improbability of fielding these in large numbers, that's probably also a non-issue.
- module_blocker1
- module_decor_midline2
- nebula - shield exactly meets collision radius at the front
- piranha
- rampart
- remnant_weapon_platform1
- shade
- spark
- station1_hightech, also 2 & 3
- station1_midtech
- vigilance
- warthog
- xyphos
- ziggurat
List four: Shielded station modules that I assume are deliberately breaking the normal rules for good reasons. (Some station modules on other lists may actually belong here, but if I wasn't certain, I put them in the appropriate 'potentially problematic' list.)
ships
- module_hightech_shield
- module_large1_lowtech, & large2
- module_midline_bastion, broadside, citadel, & support
- remnant_shield2
I agree entirely, they should drop a guaranteed pristine nanoforge, even if it means they are the only two in the entire sector, it would make them feel important and like a real treasure hunt.