Probably crispness. That’s why you score and pre-bake crusts.

It releases steam so the cracker stays flat with no steam pockets which would cause uneven baking.

With trial & error, the original cracker bakers learned that the cracker cooked more evenly with the extra holes as the hot air circulated better thereby more even cook time & a crispier cracker. Once corporations began to mass produce the cracker, they chose to not reinvent the wheel & stuck to the original recipe & method of cooking.

The best part of bread, bagels, pancakes, and crackers is the edges, because they are slightly burnt which produces a very light caramelization.
Holes in crackers increase this effect by adding more edges.