It sounds like you've researched your method well. I'm not an egg washer but I have read it can make then more vulnerable to bacteria, so your incubator needs to be extra sterile. I know bacteria can kill them off early on but i'm not sure how it would manifest further down the road - whether there is something to indicate it caused a duckling to die or if it would look no different from any other cause. Maybe you could try a batch without washing and see if there's any difference?
If you do eggtopsies are they giving you any clues at all? Do your late deaths have commonalities that could point to a cause?
The diet of your adult flock can also play a part I believe.
I know they are eggs and it's different, but from a scientific point of view I would say work your way through each variable until you pinpoint your issue. Start with your humidity (I'd probably aim nearer 40%, but that's me in my location) if your hatch rate improves a bit then play around with the levels to see where it needs to be for the best hatch. If it doesn't give a marked improvement then try changing something else.
