Help me understand this correctly, you are using arduino instead of ezo circuit to read the probe and you are pretty much mimicking the ezo i2c protocol ? If so, then yeah it should work (though remember without galvanic isolation your reading are likely to be inaccurate). Check the reef-pi log for any error. I suspect you are missing some elements in the ezo i2c protocol that reef-pi is using. If you can share a command line example of how you are getting the data in pi, we can audit it for compatibility.
Just for reference, this is the exact code we use to read the ezo data:
https://github.com/reef-pi/drivers/blob/master/ezo.go#L167 , which basically sends "R\000" and then reads 31 bytes. Make sure your code is doing just that. Another way to verify this will be to install ezo python example code and check if thats working with your setup