Addressing some of the comments/concerns in your documentation:
* To protect the ultrasonic mister from bad firmware frying it, you could probably replace R6 with a sufficiently sized capacitor to make an effective DC block
* I've also had issues with a thermal sensor just reading board temp, best solution is to make the sensor a separate board. Short of that, one can mill slots around it and reduce copper pour to reduce thermal conductivety from the PCB.
I'm prototyping my own similar kind of thing right now - an enclosure for growing culinary mushrooms - so seeing how you've used and attached the humidifier discs is really useful inspiration.
On humidification - have you considered decontamination for the water? I think bacteria and scum build up is an issue, and I've seen heavy duty equipment incorporate e.g. a submerged UVC light for trying to keep it clean. I wonder whether it's possible to do similar on a small scale by using a UVC LED (obviously need to be careful with safety though)
I may have decided on my next project!