Bans have always been used to ensure that counterpick advantage is not overwhelming, not just to avoid broken stuff.
Bans were used to stop individual characters from having an advantage in particular matchups. It was a preferential thing
centering around the fact that you shouldn't have to pick a certain character.
Marth vs. Falcon might show that Yoshi's Island is the best Marth stage and Final Destination is the best Captain Falcon stage
for that matchup. This is a
preference ban because it's not an overwhelming disadvantage to either player and its dependent on character choice. No one forces you to pick captain falcon; if he sucks on Yoshi's Island and Fountain of Dreams against Marth it doesn't mean he should have two bans.... it means he has a disadvantage because he's not as good a character.
If it turned out that Yoshi's Island is the best Marth stage for
every matchup or it was
near impossible or heavily favored for one or the other (like Fox in Hyrule Temple) regardless of opponent, this would be considered a
balance ban. It is
incredibly rare that a balance ban is left in the game, the most notable exception being Ice Climbers and FD. They had the option of "deal with it, ban ICs, or ban FD" and they chose to deal with it.
This is why Melee lost stages like Pokefloats, Rumble Falls, Kongo Jungle 64, etc.; it was to a point where Fox players got good enough that virtually everyone had to switch to Fox to play on the CPs because even if your character could play Pokefloats, it couldn't play Mute City or Kongo Jungle 64. Individually everything was fine, but in practice the preferential ban didn't do enough to allow all of these stages to exist in tournament; if you banned one, there were at least two more that would hurt your character vs. your opponent's choice.
To put it in perspective, project M has like 6 or 7 stages that are the
exact same. Flat with 3 platforms. Imagine there was a character that excelled in that environment. What would you do? You'd have to ban that character, ban a lot of stages, or just accept it. It's a tough call.
Unfortunately adding multiple bans isn't an answer because it clogs up other systems. It makes "having CP stages" irrelevant because you have to have
four of them to even pick one... which means characters who excel in the most common stage to be "the best".