I think it used to work this way back in the original beta (I wasn't around back then) and got changed because it just slowed down the game needlessly.
The biggest problem is that metal and crystal extractors are already the best form of early-game income, but dwindle in importance as the game goes on. There's no reason to make them any weaker in the late-game when they're already marginal at best.
This would also be a brutal nerf to refineries, which are already inefficient in most cases anyways. If they just cause extractors to deplete faster, then they'd be pretty much pointless. Same goes for resource focus (though it's pretty much pointless even with limitless extractor income).