How do you keep water touching sensors working long term? I tried similar sensors but they all get rusted / oxidized to work properly after a certain time.
That's what they do when performing catheter ablation (a medical procedure for curing cardiac fibrilation by destroying minute parts of muscle with electric current).
DC would work just as fine on this procedure, but due to electrolysis of water, oxygen and hydrogen bubbles would form, which could get stuck somewhere. Using a square wave AC quickly reverses the reaction every period, like you suggested for the moisture meter.
https://en.wikipedia.org/wiki/Catheter_ablation#Technique
I don't know the answer to your question, but it would be worth trying.
In small scale there is more work maintaining the automated setup and calibrating the sensors than it would take to do the measurements and dosing manually.
You’d also need to ensure the caps contained enough storage solution at the right concentration. Over time the probes would introduce drops of nutrient solution (unless you rinsed them with distilled water, in which case you’d dilute the storage solution), and you’d need to replenish it.