The V2 hat has exactly the same functions as the V3 hat, the only difference being smaller connectors and Status LEDs on the board. For longevity, that V2 hat is the way to go.
I have to V2 hats and it is an awesome product and will easily be able to implement the functions like you listed.
As far as Raspberry Pi zero vs The 3B, if you are going to run it as a headless unit without a ton of sensors and equipment, the zero will work just fine. 3B just has more muscle and LAN capability.
I use 3Bs with my build.
What exactly is meant by headless? I assumed it was access via a browser regardless.
Will the mars aqua board work with a 2 channel, 300w 32” fixture?