It's been a long time since I last played til recently, one thing that always got on my nerves is how weapons are basically an extra layer of armour for the body holding it. Is there a variable I can change for each weapon allowing bullets to pass through them? Even better if it were chance based depending on the size of the sprite, but that'd be wishful thinking.

Well both things of what you say are correct. Changing sprite to something small makes it harder to hit, Making it null is practically non-hittable.
Though... Changing sprite may bring dissatisfaction and there is an easier way to achieve this without changing the sprites.

In any ".ini" you can change this simple line from 1 to 0 and you will get your desired outcome, at "HDFirearm". Note that this also changes so that you cannot shoot it while it is sitting on the ground either.

Ofcourse you'd have to locate the .ini for the weapon you are changing.

I've tried making a Global Script that makes all weapons ignore MOs but it makes a ton of scripts malfunction, so it's not a viable way to do it.

^^^^^

A large number of scripted weapons need to find the gun, and rely on the gun being GetsHitByMOs for the projectile to effectively find it, or to easily grab the actor using it (RootID).

GetsHitByMOs = 0 makes it so the gun has no MOID, effectively breaking every scripted gun that uses MOID-based gun/actor finding.

You could probably do something a little more complex and make it so the gun's update script has a chance to remove wounds from itself and add them to the parent actor. There's probably no way to do this very well, but it's the closest thing to what you asked for that I can think of off the top of my head. I guess it might be better to get particles that are about to hit the gun then move them into the actor or something, so they hit the actor instead (or if there's a way to make something not collide with a specific MO that might work).
Either way it'd probably be a pretty heavy script to run on a lot of guns.

I already found a way to simulate the desired effect with a Global Script that sets the Scale value of all weapons to 0 and emits one-frame 'phantom' copies of the weapon on top of it each frame.

Even if you set Scale to 0, the offsets aren't affected, so everything functions the same apart from the hitbox being non-existent.

The only problem is that checking HFlipped doesn't seem to work and all phantom images constantly face to the right (while maintaining correct rotation etc.)

The phantom image also appears behind the parent actor since they aren't technically its' parent, but it's a purely aesthetic issue, like the latter.

I'll be updating my Global Script mod soon.

Have the gun's sprite be 1x1 pixel with a GetsHitByMOs = 0 attachable with the proper sprite.

It seems that HFlipped isn't assigned on the frame of creation. Other than that, my Global Script works perfectly.

I've also made a variant where the Scale value of all weapons is set to 0 every second frame. It does exactly what Morbo asked for with there being a "chance" for particles to hit the weapon, and larger weapons are naturally more likely to get hit as they have a larger hitbox.

The only side-effect is that all weapons look translucent, since they're literally only "half-there."

Could you spawn duplicates of the weapons but make them GetsHitByMOs = 0 and position them over the flip-flopping Scale guns that last more than one frame?

Would have to have a bit of tracking to check when the guns are put away in inventory/destroyed, but would look better.

I thought about doing something like that, but it's a pain to track a MO like that through a Global Script. It's still probably doable though, spawning copies with a lifetime of one frame just seemed like an easier way to do it.