I always pull the eggs apart before putting them into the tub. Less chance of cross contamination with any infertile eggs that start to rot/mold. Also, better chance that you get equal humidity/temp to all the eggs.
You don't need to worry about either of the concerns you've raised. An infertile egg cannot harm a fertile egg, and the humidity in the container is evenly distributed within the tub so each egg is surrounded by pretty much the exact same humidity.