Depends on the system. I dislike Harn's for the reason you mentioned. But I really enjoyed the system in Runequest.Or do you prefer systems that use armor pieces by location?
For example, Harn does armor pieces by location. You have head, torso, right and left arms, right and left hands, right and left legs, right and left feet locations.
Personally I prefer to use an entire suit of armor. It greatly cuts down on the book keeping.
As I am fond of saying, Runequest really offers the best compromise between realism and playability. Combat is fast and furious and doesn't require mutliple table lookups.
I'm unsure if you actually need rules supporting the use of 'mismatched' armor pieces, though. But I like systems taking acoount of body zones.