Armor should always be the best masterwork version its +X bonus allows. Some later books add additional kinds of masterwork armor, in which case any of the kinds with the a minimum +X bonus equal to the item's +X bonus should be OK, but armor should never be of a lower quality than it could be. If you're allowing players to upgrade the enchantments on a piece of armor, the armor should automatically improve to match the appropriate masterwork quality.
The masterwork armors are essentially a math fix: WotC realized player AC lagged behind monster attack bonuses at higher levels, so they put in masterwork armor to make up the difference. Consider the math for a heavy armor character without masterwork. Monsters gain +29 attack (1 per level) going from level 1 to level 30. Players get +15 (half level), +6 (enhancement), maybe +1 more from the original paragon tier feat bonuses to AC for a gain of +22 over 29 levels, a difference of 7. That means if you were getting hit on an 11 on the die at level 1, you're getting hit by a 4 on the die at level 30.