They used to do that in 2nd ed and it basically just led to everyone bunkering up in cover just as badly if not worse than they do now. The -hit modifiers from cover (-2 for hard cover from memory) were pretty brutal and devalued armour saves worse than cover does now.
If (and it's a very big if) they ever did go back to an armour modifier system then I'd rather cover gave a +1 or +2 to armour or something instead of messing with your hit chance. Though really it's more hassle than it's worth, part of the joy of third edition being introduced was getting rid of all the small modifiers and other factors that just slowed the game down.