Why does matzah have those holes?

Matzah has holes to prevent it from puffing up as Jews are not supposed to eat any leavened or puffed bread. There is no symbolism behind the holes.

The reason air pockets are a problem is because it is possible that a piece of dough inside the air pocket might not cook within 18 minutes, and will be considered leavened (Chametz) which is forbidden for Jews to eat or own on Passover. (Some groups assume that regardless of perforation, there may be pockets of not fully cooked dough in matzah; this is why there is the issue of gebrokt/non-gebrokt.)