Well, it sounds like you are talking about GROUND vias between two ground planes on different layers. Many separated vias are used to keep the impedance as low as possible and to break up large loops into many smaller, less significant loops. For every ground connection, you will want as short a distance from the system ground as possible. If you were to use only one large via, the distance from system ground would go up, possibly causing problems, even though the total copper connecting the ground layers would be the same. Also, the could now be many large ground loops the could also cause a problem.