Your setup looks fine. I really wouldn't worry about airflow or air exchange too much. If you open the box for a minute or so once a week they'll be fine.
Unless your egg boxes are completely 100% air tight, you won't need to add air holes. Even those shoe boxes that have a tight seal still allow some air exchange.
I would suggest picking up a hygrometer. Even a cheap one is better than nothing. You should be able to find one that also has a thermometer on it also.
I use a digital thermometer/hygrometer combination. It has two probes and an external readout. I usually place this in the egg box that is in the center of my incubator. The only hole or gap in my egg boxes is the one I made to fit these probes into the box.
Using this device along with my temp gun allows me to keep a better eye on my eggs and setup. Usually the egg boxes that do not have the thermometer probe in them have only about 1/10 to 1/2 of a degree temperature difference.
Using water only in your setup is fine, but when you add water be careful not to splash. This is the main reason I add perlite or vermiculite under my egg crate. It helps to reduce splashing when I add extra water (using the no substrate method allows you to add as much water as you want so there is no measuring or ratios to worry about). Also, I have three kids and sometimes they do bump my incubator, even though it is in a safe room, mixing in the substrate gives me one less thing to worry about. I've also found that the water evaporates slower in this type of setup.
Don't take this the wrong way. Mixing substrate is just an option, not a requirement. Personal preference dictates whether you decide to use it or not. From what I can see your setup is just fine.
-----
.
.
.
.
Stay United!

"...I say 'apparently' because despite all our progress she is not at all a tame or handle-able snake and gettting her from that cage would re-start a war.. and we've had a good armistice for several months now."-Gus Rentfro - I love this quote!