Yes, of course 2 heroes>1 hero, but here's the thing: let's compare winston stacking to stacking other heroes.

Stacking Pharah has more damage, more splash, etc. You'll probably have pretty good vertical control. However, Pharah's problems still remain (e.g. a weakness to hitscan). Let's say you stack someone like Tracer. You still have Tracer's weaknesses of being vulnerable to being instagibbed and the like. Stacking these heroes doesn't necessarily help with their weaknesses.

Two Winstons, though? One of Winston's biggest shortcomings is that one of them isn't potent enough to be a killer, but mostly a disruptor. His shield has a high cooldown, his gun, while easy to aim, only does 50 dps, and if a team responds, they can chew through one winston before one winston can kill someone. He's all right, sure, but he has his flaws. But when you stack him, those flaws are alleviated. 100 dps is a lot more respectable, ESPECIALLY when the enemy team has two winstons to chew through. The shield also helps as well. More shield uptime means that Winston's a lot better at isolating a target. Compare that to stacking 2 Bastion or something ridiculous like that. Yeah, bastion has crazy dps, but he's still immobile and vulnerable to corner peeking, even if there is two of them.

To put it in short, stacking Winston helps him overcome his shortcomings as an individual hero. It's not just 2>1. It's more like 1+1=3. They synergize with each other well, moreso than it would be for stacking other heroes.