Reptiles don't use nearly as much air as mammals do. They will be fine in the incubator for 24-48 hours. The biggest concern is moisture as they need a lot of moisture in order to have their first shed so you just want to make sure they don't dry out in there.

Most likely you will go to ventillate the container one day and a baby gecko will be sitting in there looking at you. They hatch fairly quickly so unless you happen to be watching when they start you probably won't catch them in the act.