I've frequently heard the Basic Role-play system and Dark Heresy described as deadly from a combat perspective. I think those are both percentile systems. Is that typical of percentile systems or is there something statistically more dangerous?
BRP is "deadly" mostly because the damage capacity is relatively low (Size+Con)/2, averaging 11 points, and damages are a significant portion of that. Weapons range from 1d4 (dagger) through 2d8 (Greatsword) damage, before accounting for damage by location limits and impaling... and head hits can only take 1/3 the total. Quite simply put, a single hit in the head with any weapon has the potential to kill the average character. Even the toughest humans only have 6 HP in the head. All damage to locations is also marked against total hit points. And a Critical hit bypasses any worn armor, and does maximum damage. If head or chest are depleted, dead. If total hit points are depleted, death also occurs. Also, even the best of normal armors (8 point full plate) is within reach of being penetrated by a broadsword's 1d8+1+DB - a strong man can do up to an additional d6, making his d4+1 dagger into d4+d6+1 - 6/24 =25% chance of getting past armor (Str+Siz>32 - 16 each is big and strong), and a slightly above average guy (13 each) gets a d4 Damage bonus for a 1/16 (=6.25%) chance of getting in. A serious fighter can be lethal to even armored knights.
Dark Heresy is far less deadly. Wounds starts between 8 and 15, most weapons do 1d10 to 1d10+5, tho' some exceed 3d10, and running out of Wounds points doesn't kill. (In fact, one has to go at least -7 to stand a chance of death.) Further, the first 2-5 points of each hit won't count, as the individual's Toughness Bonus plus armor value will be subtracted. There are no location hit points, only the general pool; the location hit determines the effects of being negative and which armor applies. Most characters can survive even a full burst from most weapons.
Looking at Rogue Trader (since it's to hand), autofire is a +20, and each 10 points made by is an extra hit (to the limit of rounds in the burst) - so, joe average is 60%, Mr. Marine is probably around 75%, and the wounds and armor are as per Dark Heresy - 8 point power armor and a typical RT character's 45 T would soak 12 points per hit, and the fairly typical mesh of 4 means they soak 8 points per hit; an autogun doing 1d10+3 per hit, and hitting up to 5 times (tho, typically, only getting 2-3 hits) is still doing only 8 points average per hit... half the hits do nothing versus even moderate (and mesh is moderate) armor. Without righteous fury, Toughness 50-60 marines in 8 point power armor are walking tanks - and ignore anything. Righteous fury is required in order to take them down. At least, until the armor ablates away. Note that any weapon that does more than the Armor Value, even if the rest is soaked by Toughness bonus, reduces armor by one in the location hit, and so eventually, Mr. Marine has no armor left. It never rises to the D&D level, but it can get pretty epic, especially in Deathwatch. Autofire isn't deadly to well armored characters, but it sure can remove that armor quickly, resulting in significant injury.
Lethality is more a function of damage mechanics and the ratio of damage capacity to damage done than skill mechanics.
pre-4E D&D, when played at low levels (1-2), is as deadly as BRP. Weapon damages up to 2d10, Hit points of 1-14 at 1st level, and as many again each level thereafter... with only 4-8 per level being typical. (Far less for wizards.) And, as written, death when below zero. Armor makes it harder to be hit, but any hit still does full damage.
At high levels, that means hit point totals up to 150 HP... but damages don't go up.
Moreover, armor is usually better at higher levels, so fewer hits are obtained.
So, at low levels, D&D is deadly; poor armor means getting hit more, and every hit matters. At high levels, it's not deadly; good armor means fewer hits, and the hits are a far lower percentage of the total, so characters can become damage sponges. And in between, it gets less deadly with every level.
No, this is not an inherent trait of d% systems, but a result of the exact mechanics. BRP is descended from RuneQuest, which was designed to be more realistic than D&D: Thus, characters only have a few hit points. It has also been used for games such as the Call of Cthulhu, which value players being unable to always fight their way out of situations.
Similarly, Dark Heresy is designed to have you play as the low powered pawns of the Inquisitors, and thus likely wants a brutal combat system. (I suspect if you go to Deathwatch then you will have a significantly less brutal game, though I have no experience with the line.)
You can demonstrate that with no modifiers a d% is equivalent to a d20 (1 in 20 = 5%, proof left as exercise). You could actually work out the % of any roll in D&D and use d% to roll it if you felt like it. Therefore, there is no mathematical reason that d% games have to be more lethal; it is just that the most popular games to use that system happen to be quite lethal.
The real reason BRP is so lethal (I can't speak to Dark Heresy as I haven't played it, but I know BRP rather well) is that it is very easy to get good with weapons but your hit points never rise. So characters will very quickly get quite good at inflicting damage, as will their foes, but they never get better at absorbing it (or only do so slowly, as they get better armour). They do get better at dodging attacks (Dodge and Parry), however if you do get hit you aren't any better at absorbing it. If your HP rose as you gained gained in power, as you do in D&D (the 'baseline' system) then BRP would not be any more lethal then D&D.
(I'm ignoring major wound and hit locations as they are different in each implementation of the system, and are thus demonstrably a part of the individual system and not a trait of using a d% as the base die type.)
Paranoia is the highest lethality game that I know of: dying and activating your next clone is one of its tropes, critically failing a single roll is likely to get you killed, and dying multiple times in a single session is common. It's a d20, roll-under system, not percentile.
The Riddle of Steel by Jacob Norwood and Driftwood Publishing. May be out of print currently.
The game is inspired by the Conan stories, and the system is intended to emulate medieval combat plus wicked awesome sorcery. Supposedly the guys who designed the game actually know how to use swords and armor and based its combat system around this knowledge.
Combat is brutal, but is also tactical – in a fight between two fairly matched combatants you can still have someone dead at the end of round 1 if a poor choice is made, or the dice are not in someone's favor.
Sorcery is just ridiculous – and I mean awesome. It uses the old dark medieval association that sorcerers are not to be trifled with, so think of Merlin and Gandalf and Belgarath, not Fumbles the 1st Level Wizard. No magic missiles here, just vagaries, which define how sorcerers can impact their targets.
A system that I have found to have a high mortality rate (pending certain basics) is L5R. Thanks to the fact that it works with a "Hit Point" type health system, and the "exploding dice" mechanic (it's a d10 system, where if a 10 is rolled, another die is added to that die's total until it stops rolling tens) lends towards no upper limit of damage other than that 10-X chance you'll explode again. In the beginning stages of the game, a character might have only 32 "wounds" before they are dead, and even a non-kill gives that character penalties. The basic katana has a base of rolling five dice and keeping the highest two (keeping in mind that all 'explosions' based in a given die count as part of that die). In short, unless certain precautions are taken, builds that are not combat/damage driven can be quite terminal.
This isn't system inherent, it's really based on the setting.
For instance, in Eclipse Phase it's totally possible to have mostly non-lethal combats with no real chance for any side to do major damage, and it's a percentile-based system. Doesn't mean that it's less deadly, but the combat's quicker.