The real answer is that all attacks are based on penetration and contact area (and to a lesser extent velocity).
The game doesn't recognize the difference between "slash" and "stab" and "bludgeon", only the values that each attack carries. I suspect Toady may modify the properties of attacks at some point so the effects of different moves are better realized.
I am aware that the names of the attacks are only used for creating logs, and have no impact on performance. I am specifically wondering if anyone who's been around for a while knows why Toady decided to make stabbing attacks have a lower penetration depth than slashing attacks, as this is contrary to what one would expect in the real world.
My best guesses are either:
a) A game balance issue - at some point he found stabs were too powerful, and lowered penetration depth to compensate.
b) An oversight. However this seems unlikely as it is consistent across all stabbing weapons.
c) I don't understand how penetration depth is interpreted by the game. I thought it was the maximum combined thickness of clothing, armor, and tissue which could be penetrated by an attack, and that long pointy weapons (like spears) have a higher penetration depth than shorter weapons (like knives).
So far I would say the most sensible answer is
If I'd have to think of a reason, it's could be a balance thing. Slashing attacks have a much harder time penetrating than the tiny contact areas of stabs, so if the wielder just happens to be a musclebound hulk that can make the most of it, he's earned the extra depth. The "Conan cleaving dudes asunder" effect.
...
In other words, slashing attacks are not limited by penetration depth at all, but rather by whether the attack has enough momentum (due to the attacker's strength, etc) to cleave all the way through the impacted layers. Due to the very large contact areas of most slashing attacks, they generally will not be able to penetrate deeply because it costs too much momentum to penetrate such a large area of armor/tissue, and in general will penetrate less than the stabbing attacks in spite of the larger penetration depth. However if you are really strong and/or hit a smallish body part (effective contact area is the smaller of the weapon contact area and body part size) you might be able to go all the way through and cut off the body part.
I am pretty that the standard penetration depth of swords (2000) is enough to penetrate most humanoid sized body parts (I've certainly stabbed people in the heart with a long sword), so this really only comes into play for attacks on large creatures. This may have been added so that you can't stab a dragon/hydra through the heart with a short sword.