I did a quick sketch what do you think?
If the top is closed, it doesn't follow Henry's law any more since it's an enclosed atmosphere? It's like a drop checker at that point.
Exactly! It is just like a drop checker but you are measuring CO2 directly rather than inferring it from a change in pH. Why do you say Henry's law wouldn't apply? With a drop checker, you have two aqueous solutions connected by an air passage, so the concentration of CO2 in the tank water equals the concentration in the test solution since they are both aqueous. If you measure the CO2 concentration in the head space, you have to calculate the concentration in the water using Henry's law. As long as bubbles of CO2 (or any other gas) aren't constantly rising directly into the test chamber and the pressure within is equal to ambient air pressure, the concentrations of gasses in the head space should reach equilibrium with the concentrations of gasses dissolved in the water at the ratios described by the Henry's law constants for the given temperature and pressure. You can't have the head space open to the atmosphere because the concentration of CO2 in the tank water is greater than what you would have at normal equilibrium. The tank is constantly outgassing CO2 into the atmosphere trying to reach that equilibrium like a big glass of carbonated water fizzing its CO2 into the air. The room will never reach equilibrium with the tank unless it is sealed because CO2 is constantly diffusing away. The head space must be sealed to reflect the concentrations of gas in the water below it.
I would not clamp the test chamber to the side of the tank but rather build a floating platform so the pressure in the head space does not change as water level rises and falls. This could be as simple as an up side down plastic cup pushed through a piece of Styrofoam. In my opinion the use of a membrane of any type will only slow the response of the sensor (which will always have some lag as is).
This is a really cool idea. I just think it can be executed more simply without the dry box and silicone membrane.