The reason is, that your egg boiler recycles the water a couple of times.
You say that the process is finished when the water is gone, so you are talking about an egg boiler that cooks the eggs with steam. In these egg boilers you have a shallow, heated pan at the bottom into which you fill the water. Then the egg boiler boils this water at a constant rate (the heat input is constant, as the pan will remain at 100°C for the entire time and is electrically heated). So a constant amount of water is boiled off per second.
Now, above the water you have the eggs. And here comes the difference: If you put a single egg in, it has a certain surface on which the water condenses. This condensing is slower than the steam production, the additional steam just escapes through the hole in the top of the cover. The more eggs you put into the steam, the larger their surface, and the more water will condense on them. This condensed water then drips down back into the pan, and is evaporated another time.
As the steam production remains constant when you increase the number of eggs while the water condensation grows, less steam escapes through the hole in the cover. Thus, the water loss is slower with more eggs.
Now, to get well-cooked eggs, you need to heat them for a specific time. And because more eggs keep the water inside the boiler longer, you must reduce the starting amount of water to get the same cooking time. That's it: You reduce the amount of water to keep the cooking time constant.
I confess, I simplified a bit: I ignored the condensation on the inside of the cover itself. I did this, because that condensation is independent of the number of eggs. The condensation on the cover simply serves to quickly heat up the cover to some temperature slightly below 100°C, and then just supplies the heat necessary to keep it at that temperature.