[SixOfSpades]

Actually, the number IS a percentile: Having 100% in Open Locks means that you are guaranteed to open any pickable Lock (one that does not require a specific key, wardstone, or plot event) on the first try. The same goes for Set Traps, Find Traps, and Detect Illusions.

As for modifiers--you bet they're there. The most obviously modified skill is Pick Pockets: With 100% in the skill, you can sneak around at night, pilfering from all the Commoners you want, and the only way you'll get caught at it is if you happen to roll a 1. However, all of the following cause penalties to your Pick Pockets score:
Pickpocketing in broad daylight
Pickpocketing while Fatigued
Pickpocketing officers of the law (Amnish Centurions, etc.)
Pickpocketing other Thieves (ever tried going through Renal Bloodscalp's pockets? Good luck!)
And, most of all, Shoplifting. Stealing from a store imposes MAJOR penalites to your PP score--regularly, as much as 100%.

Stealth and its two composite skills, Hide in Shadows and Move Silently, take penalties for the following:
Trying to hide (or stay hidden) where there's no cover (open meadow, the middle of a huge empty room, etc.)
Trying to hide (or stay hidden) in broad daylight or other bright lighting conditions
Trying to stay hidden with Hostile creatures in your sight range (the penalty is added with every hostile creature)

As for penalties added by armor, don't confuse the Thieving penalties caused by wearing Elven Chain or Hide Armor (which were implemented in the game) with those caused by wearing Leather or Studded Leather (which, I believe, were not). Just because the Manual says that Thieves can get relative bonuses to their scores by parading around naked doesn't neccessarily mean that it's true: After all, the Maunal also says that Bards can Read Languages, Detect Noise and Climb Walls.