Yes, you can import and export the same Pokemon in Box. But it will not increase the number of Pokemon deposited.
The number of Pokemon you put or retrieve from Box are solely stored in the game cart. Nothing about how many Pokemon you have put into Box from a cart is stored in the gamecube memory module of Box. Only the Pokemon which are in Box are stored there.
On a game cart there is some kind of a Pokemon Box counter. Whenever you put a Pokemon into Box this counter increases and, of course, whenever you remove a Pokemon from Box this counter decreases.
So, you will only get the Box Eggs when this counter has reached a certain value.
100 Zigzagoon
500 Skitty
1499 Pichu
And when you first connect your game cart to Box you will get a Swablu.
Notice that when you first connect your game cart to Box this incident (and whenever you get an Egg) is stored on the game cart too. Even when you put or retrieve no Pokemon from Box you will not get a second Swablu Egg after you reconnect your game to Box.