A small hole in the lid should not hurt the process; CO2 being heavier than air, it would settle to the bottom of the container fairly quickly.
Unless the container is airtight the gases will diffuse down their concentration gradient to equilibrate the concentrations inside & outside the sealed containers. If this were not so we would all be walking around in a thin layer of CO2, underneath a layer of O2 underneath a layer of N2. There would be a layer of methane covering my bedroom floor in the morning.
If you have a small hole in the top the system could be improved by adding an airlock - a cheap piece of beer brewng equipment.
I was really interested to see this thread as Ive disposed of pest rats & mice for years with a similair system made using vinegar & bicarb - a cheaper but slightly messier option than soda stream. I think I'll buy a soda stream.
One final comment. I haven't got around to it yet, but this system could easily be upscaled to humanely kill feral cats - a beer brewing fermenter would be the perfect size.