Well remember, Hansen (I'm thinking that's the right Admiral) said the Klingons were sending ships. So it's likely that the Klingons got late to the fight and scooped up some survivors, along with whatever surviving starships did as well. Then, as Voyager informed up, we know some captives were taken and shipped back to the Delta Quad. So it's very likely that it's was a combination of the three things that lead to the area being vacant when the 1701-D rolled up on the scene.
Here's a ghastly thought, how many people in those escape-pods committed suicide upon when they saw the battle doing south, thinking they were going to be assimilated.