If you learn Lambda Calculus, you probably already know that λxy.y arg1 *arg2* will reduce to arg2, since the x is replaced by nothing, and the remainder (λy.y) is the identity function.
You could write zero in many other ways (i.e. come up with a different convention), but there are good reasons for using λxy.y. For instance, you want zero to be the first natural number, so that if you apply the successor function to it, you get 1, 2, 3 etc. With the function λabc.b(abc), you get λxy.x(y), λxy.x(x(y)), λxy.x(x(x(y))) etc., in other words, you get a whole number system.
Furthermore, you want zero to be the neutral element with respect to addition. With our successor function S := λabc.b(abc), we can define n+*m* as n S m, i.e., n times the application of the successor function to m. Our zero λxy.y satisfies this, both 0 S m and m S 0 reduce to m.