I would not make any holes in the egg box. The Hatchrite has just the right amount of water for the eggs. If you make holes you will lose moisture and there won't be enough for the eggs. Water can drop on the eggs a little without doing any harm, you just don't want it to happen to the point where the droplets are not evaporating or are dropping on the eggs constantly.

I wouldn't worry too much, but you can hot glue a piece of cotton or other material, like part of a t-shirt to fit the inside of the lid so it absorbs the excess water so it doesn't drop on the eggs. Or you can put a plastic bowl or other dome over the eggs to the condensation runs down the sides and back into the Hatchrite instead of dripping down onto the eggs. I get condensation that drips onto the eggs, but I don't worry about it, I just leave them alone until they hatch, and I haven't had any problems; no mold, nothing, but I also do substrate-less incubation. Good luck.