I've never liked that argument. If there were sources of oil, honey, or gas out in the world that you could, theoretically, collect with a container then you can be sure people would have complained about the absence of those hypothetical containers. Jars are a completely different (IMO) thing because they could be used to collect water from the world. Games, survival games in particular, should strive for as much realism as possible.... and to have a game where you can see bodies of water that you can drink from, but for some reason can't collect feels very removed from reality.
That said, I'm not really all that opposed to their removal; water was far too easy to collect. But lets be honest about it, they were removed to make water more scarce.... not because "that's how everything else works"
The removal of jars, and the inability to get water from a lake are **independent** changes. If TFP wanted to change the game so you could collect water, then you would instead of drinking it directly get 10 **jars** of water into your hand directly (or into the inventory). Still no empty water jars in the game, but you would get water from a lake.