The 12V power supply in original BOM has maximum output of 30A. This 12V PS is needed for 90W grow LEDs and approx. 10W (2 meters) for white LEDs. Maybe Arduino can be powered from this source (let's say another 5W). Both ventilation fans should be 8W. So 113W in total. It means there is 360-113=247W left. Your Peltier element will take another 60W, so there is still 187W remaining.
As for relays: I m not sure either but maybe one is not used (?). But be careful, the electromechanical relays are not designed for huge DC currents (also, they are not designed for fast PWM). The better choice is to use MOSFET transistor, for example IRLB8743PBF (I used them for 10A switching, PWM, no heatsink, without any problem).
Interfaces: There are three interfaces which are commonly used in Arduino world -- serial (a.k.a UART), I2C and SPI. The Arduino have several serial (UART) interfaces so this can be used. I2C supports several slaves on one bus and right now, only one slave is used.
I2C was designed for short "inter-integrated circuit" communication, thus small distances -- few centimeters. In my last project, I used Modbus over serial line. This is very simple, bidirectional master-slave protocol with CRC checking. It supports up to 248 slaves on one bus and if you use RS485 (differential signals) you can use it on long distances too. Without RS485, you can use it on plain UART. I think Modbus is good choice, because it is easy to make design more modular.
If you are interested, I can help you with implementing Modbus. I have Modbus bootloader and simple client code for ATMega88/168/328 AVR family.