Torque is a finicky thing and not the most accurate way to measure fastener preload. That said, it is the most convenient method for mechanics to use to install nuts and bolts, so that's what get's used. With that said, Steve83 isn't wrong as far as what the OEM's suggest about "clean, dry threads" for torque specs, however how many of us have clean, dry threads? I don't intend to swap out my wheel studs and lug nuts every time I remove my wheels and tires with new OEM parts, so I use anti-seize to keep everything happy...mostly myself.
Most modern wheel studs and lug nuts use various anti-corrosive plating (mechanical zinc plating) options with high-pressure lubrication and self-healing properties. Most of our rigs have no such thing and have either plain or electro-zinc plated fasteners, which have much lower corrosion resistance and higher friction.
There are some pretty good fastener engineering books out there are both interesting and informative if you're into that kind of thing. That said, for how prevalent screw type fasteners are in everything, there's still a lot of room for interpretation. At the end of the day, it's all about achieving the proper preload/stretch...if you can do that, you're probably golden. Vibration, galvanic corrosion, and other concerns can crop up and cause unexpected problems. I guess if it were simple, you would just have some torque tables and call it good, but instead you have engineers who's sole purpose is to design and apply the appropriate fastener to the appropriate application, and even they get it wrong sometimes.