I've used holes and no holes, both can work well. Some people have been using holes for decades and swear by it. There is a hundred and one ways to do it well, some of those ways use ventilation in the tubs. Obviously you have a method which works well for you and that's fantastic, but it's not the only one.
Rotting eggs would indicate the moisture level is too high, assuming temperatures are good and there are no other problems (impossible to be sure of from the information here, but moisture and temperature are the two biggest issues in the majority of cases).
For gecko eggs, and reptile eggs in general, vermiculite is fantastic if you know exactly what you're doing and you're going to closely monitor the situation and adjust as needed if needed, but otherwise it's dangerous because if you don't get it right it is quite unforgiving. I spent about 5-10 years using it exclusively, then for about 10 years I experimented with various things, and eventually, despite becoming quite good at getting vermiculite just right, I stopped using it because while I could do it, it required me to spend so much time getting it exactly right and sometimes make tweaks mid incubation, as opposed to the idiot proof 'set and forget' options which are almost as good as perfected vermiculite but with almost no effort in setting up or monitoring. It was funny to spend years becoming good at vermiculite then abandon it anyway. I stopped experimenting with media over 10 years ago now.
One common mistake with vermiculite is to make it too wet, because it is hygrophillic (it loves to absorb moisture even from the air) and if it already contains some moisture, when you weigh it, you don't just add water to the vermiculite, you add water to the water which is already there. The 1:1 ratio only works well if you start with very dry vermiculite, and going too wet is more dangerous than going too dry. You can go a bit more dry than perfect without an issue, but you don't get much more moist than perfect before you'll kill your eggs. Vermiculite gives you extra control, which is fantastic if you know what you're doing and bother to do it, but other methods (like perlite or suspension, which in practice are basically the same thing) give you a consistent result regardless of how much water you add (it's funny when people carefully measure water with things like perlite, when it makes no difference to the incubation conditions as long as it's something between a little bit of water and water actually sloshing around in the perlite, and even then you'd probably get away with it as long as the eggs weren't touching the free water).
