This is just my theory or what not.

I'm guessing the piercing damage type originated from the "toothpick" swords. I mean it would make sense since they're basically rapiers. These are swords that specializes in thrusting (not that type of thrusting) its pointy end to do some serious damage by piercing through the enemy's body (see what I did there). Unlike regular swords it inflicts damage by hacking through the enemy with its edge.

With this in mind it seems reasonable for these "toothpicks" to easily poke through these squishy beasts and into their vital organs. I guess this works with silkwings, devilites, I don't know about trojans. But how would it poke through metal? I guess this is why they resist piercing damage. Plus same thing with slimes, nothing really happens when you poke them, have you tried to poke Jell-O with a toothpick, nothing really happens.

However my explanation doesn't make sense with piercing guns. Especially with the Riftlocker, look at its description:

"A deadly handgun said to be capable of sundering heavy armor with a single shot. These firearms proved instrumental during the siege of Isora in breaking through the war machines of the Morai."

Whaaatt?????
If the game says constructs resist piercing damage why would the description be this? Maybe the devs just wanted piercing guns since it would have been weird with just shadow and elemental guns.

Honestly I wouldn't think about this too much, after all we're in a game that gives you bonuses by wearing some kitty kat hats.

Fun fact: flourishes were not in the game at launch. Piercing damage thus can be assumed to not originate from there.

Pierce I assume is still a sort of poke thing however. All original pierce weapons relied on a sort of splinter mechanic - ie, if you stab something with it, it'll go into it.

Piercing is not effective against constructs due to constructs having metal plating. The "splinter" thus sort of... bounces off.
Piercing is not effective against slimes since slimes are more of a single cell organism. When you poke them they just sort of glorp back together with no real damage. The only way to hurt a slime with a piercing weapon is if your poke was fast enough to break the surface tension AND still be going fast enough to hit their core do-dads. Meanwhile, shadow damage just sort of melts them.

Beasts and fiends both have very light skin. This makes them highly susceptible to piercing damage. Gremlins have thick and unruly fur, and on top of that, likely thick clothing due to all of their construction and deconstruction they do. They aren't strong to pierce but aren't weak to it either.

At least, these are all the reasons I've sort of thought up for it all. Makes sense to me, but I remember someone wanting to reclassify gremlins as "weak to pierce", and that sort of makes sense, but with a trio of damage types and a sextuplet of monster families assigning 2 to each makes sense.

Normal vs everything- Hack, slash, stun
Piercing vs Construct- Pokey spines bounce off of metal. Plink, plink, plinkplinkplinkplink
Piercing vs Jelly- Pokey spines just stick into the jelly and don't smash it or dissolve it. Glorp.
Piercing vs Gremlin- Metal armor but soft bodies. (gremlin noise)
Piercing vs Undead- Bone splinters, cloth gets holes in it. blargh
Piercing vs Beast- just go hunt something with a spear and tell me it doesn't work.
Piercing vs Fiend- THE LIGHT OF TRUTH PIERCETH ALL WHO ART UNWORTHY. ABANDON THY WICKED WAYS BEFORE THOU BECOMEST AS FODDER FOR THE CANNON; AS PREY FOR THE ARROW OF LIGHT THAT SOARETH THROUGH THE HEAVENS AND STRIKETH TRUE ON A COAL-BLACK, DESOLATE HEART, HOLDING FAST EVEN AS ITS TARGET IS RENT ASUNDER INTO THE ASH AND BRIMSTONE OF THE ONE TRUE HELL. SEEK SALVATION QUICKLY, LEST THOU BECOMEST OVERRUN AS THE HOLY CITY TO THE BARBARIAN HORDE.

Any questions?

As far as Fiends are involved, could you corrupt them more than they are already corrupt in the first place?

Piercing - Physical force concentrated in a small target area, with the aim of penetration (Blitz Needle, Splinter Bomb)

Elemental - Manipulated natural energies like heat and electricity (Glacius, Storm Driver)

Shadow - Otherworldly destructive energies (Gran Faust, Graviton Bomb)

Piercing:

VS Beasts: Beasts don’t wear armor. Piercing attacks can penetrate their elements-resistant hide rather easily, causing internal injury. (Effective)

VS Fiends: Save for the ties worn by Pit Bosses, Fiends don’t wear armor either, and they presumably don’t even have hides like Beasts. See above (Effective)

VS Gremlins: Gremlins wear cloth armor that stops pierce attacks only to a certain extent, though it presumably provides good protection against Cradle’s elements. (Normal)

VS Undead: IDK

VS Construct: The metal plating of constructs is relatively harder to penetrate, reducing eventual damage compared to other monster families. Furthermore, internal circuitry is not damaged as much by small holes than, say, extreme heat or electrical surges (Ineffective)

VS Slimes: The heavy viscosity of Slimes’ outer layers excel at stopping physical penetrating attacks by slowing them down drastically, lowering overall injury. Also, it suffers less injury than Beasts as it lacks internal organs that would suffer from penetration (Ineffective)

As an afterthought, the reason as to Shadow attacks’ effectiveness is probably due to Slimes’ outer layers and Gremlins’ cloth armors, though adapted to Cradle, being more unequipped to deal with such otherworldly energies.

Piercing vs Undead : normal damage

This could be stated in a much clearer way, that doesn't involve the phrase "normal damage".

How shadow energy work, by MDJ's head canon:

Shadow energy is the opposite of mist energy, while mist energy built up most of the clockwork that you see in the game, shadow energy do present in the form of fiend, undead and the swarm.

Raw swarm energy cannot be used by any spiral tech, since it is an energy of pure chaos and destruction, anything built from the swarm will collapse almost immediately due to its construction defies real world logic. However, at a limited quantity, shadow energy can be fused with mist energy based material on a more permanent basis (ie, acheron and gran faust).

So, what to all of this have to do with its effectiveness against slimes and Gremlins?

Slimes - their body are mostly consists of homogeneous fluid, shadow energy has a tendency of nullify and repel any mist energy that comes into its vicinity, with swords like acheron, the swarm energy forms a field around the blade and as it cuts through the slime, the swarm energy react violently with the slime's single celluar body, causing it to burst and loose its surface tension. This explains why the dark energy is neutral against beast and construct since their body structure are more complex. Fiend and Undead are consist of dark energy too so the blade wont cut through as easily.

Gremlin - Gremlin was once the creation of the core, but Tinkinzar, saw the fate of the Almirian empire and knows that his kingdom is next in line to fall decided that he was going to defy the will of the core and live on his own accord. For this end, he trapped the will of cradle into the metal shell of the core, effectively taken over as the ruler of cradle. As retaliation, the will of cradle marked the entire Gremlin race for death, swarm, obeying the will of cradle, seek out and destroy Gremlin wherever possible. So in another word, we are doing the swarm's job.

Someone probably already said it, but:

You can't stab robots because they're metal
Slimes are like rubber. They're too squishy to stab, they stretch with the blade and they self-heal from pokes.

Beasts are weak to piercing because stuff like bear traps and arrows and the stuff you usually would kill wild animals with.
Fiends....well beats me, actually.

The Swarm is actually the opposite of The Core, and probably the real reason why it was stated that Tinkinzar technically "betrayed The core was so he could harness the Swarm by himself; as to what Herex did.

'betrayed' could be understood in several way, the founding fathers betrayed the British to establish united states of America. And I don't recall anything stating in the lore that Tinkinzar knows how to harness the swarm, only Herex. To quote from one of his message:

Herex no longer serves as one of the Nine.
Only Herex sees and hears the Truth. Only Herex will prevail.
Follow Herex and you will be spared.

Speaking of Vanaduke, most of his guard, the zombies, are weak against elemental damage, and elemental damage is bread and butter to Gremlins, how do you explain that? Perhaps Tinkinzar knew not to mess with the core and Herex, being a bit of a prick, decided to go against it?

Or a skull, so to speak.