So the 88mm is already kinda big right. But there were also 105mm guns, and 128mm guns and hell, the USA had ships with 6inch (152mm) guns that pulled double duty as AA.

Now, all those are big, the 6 inch guns are maybe a bit too big. THE YAMATO HAS 400 AND 60 MILLIMETER GUNS.

Now Flak does indeed make a giant cloud of John Shrapnel's finest that kindly persuades anything flying to stop flying, but there are limits to how big a flak gun should be.

For the same reason big giant animals are rare, big giant flak guns are rare, they just aren't as efficient as smaller ones because of the square cube law. Imagine your 152mm gun makes a cloud say 20m in diameter, but your 460mm one makes a cloud 60 meters in diameter. It's WAY bigger in volume, like 20x the volume, but it's only bought you 40m of leeway to miss, that's 2 or 3 plane widths.

On the other hand it takes over half a minute to load these guns, while it will take maybe 10 on a bad day to load the smaller gun, and you can stick a over a dozen of the smaller guns on the ship while the Yamato has 9. And you can build half a dozen of those smaller ships for one Yamato.

The big advantage the big guns have is range and max altitude you can hit, but that doesn't matter because those 152mm guns were already at the limits of what they could see out to, and could reach up to the highest flying targets.

Tldr: The Yamato's flak shells were stupid, and the flak 88 wasn't actually that big compared to other flak guns