To be honest, there isn't much evidence there really were thousands of eggs on the Derelict. We sure don't see thousands when Kane is down there, and Ripley herself was never down at the ship to see thousands. In fact neither Dallas nor Lambert were down there either (they used the cable to pull Kane up). Kane was the only one down there and he didn't remember anything.
So I don't know where the "thousands" came from since nothing in the first movie even implied that.