Yes, I would be concerned about not feeding too many unhatched eggs. Though I also think that the fish will mainly go for the live and kicking artemia nauplia, but as you say still …..
I have not many very good ideas, but I always do it like this : after having harvested the nauplia, I put them in this little container, which I then (if I can see there are many unhatched eggs) leave to stand for a little time, perhaps five minutes. I place the container near some light, sometimes just pointing a flash light on the side of the container. Then it becomes quite obvious where the live artemia is gathering and you can then use the little syringe.