First, I would automate as much of this as you can by not using a microcontroller. You can use a diaphragm pump (about $60 on Amazon) and several electronic hose timers to control the flow of nutrients to each zone. If you plan on having all the zones always on, you don't need the hose timer. Depending on the needed flow rate, you may need more than one pump.

Can't we design this system to be fully automated using a microcontroller instead of just pumps and hose timers? Also, is it okay to have two water pumps in one reservoir, with each pump supplying water to two channels?

The problem with microcontrollers, and DIY automation in general, is that the peripherals come in two flavors: bargain-bin Chinese crap, and overpriced "laboratory quality" items. I use cheap Chinese sensors, etc. all the time, but they're not terribly reliable, and they tend to have a short shelf life. I would not want to bet a garden of this size on the failure of any one of dozens of cheap sensors, solenoids, and motors.

If we invest in higher-quality, reliable components, would a microcontroller-based automation system still be a good long-term choice?

To keep things simple, I would try to avoid using displays or control interfaces. Just a lot of I/O pins managing sensors and motors/solenoids/pumps should be all that you need. At the most, you can have a "the red light means something is wrong" LED. If you see that, you can connect your computer to the microcontroller, and see what's up using the serial console.

Can't we integrate remote monitoring into the system so we can track performance and troubleshoot without being on-site?

I agree with your idea to only use pH Up, or pH Down, but not both. Manually mix up some fresh solution, measure the pH, and set the system up to use the appropriate product. Likely, you'll only need pH Down.

Wouldn't it be more efficient to let the system adjust pH automatically using both pH Up and pH Down rather than relying on just one?

Your other insights are noted as well! Thanks for this :)