I think you are confusing the RJ45 CONNECTOR with an Ethernet connection. The emonPi does in fact have two RJ45 sockets, one is Ethernet (labelled as such) and the other is simply an 8-pole connector which is used for the pulse and temperature inputs. This one is clearly labelled "RJ45 I/O - DS18B20 - IRQ/PWM.
The answer is, using your suggestion, they would not be. The emonPi has only one pulse input while it also has the radio module. It can never have three. You cannot do it the way you suggest. The best suggestion I have is to use a separate Raspberry Pi and connect the optical pulse sensors directly to the GPIO inputs.
This is for 2 sensors and a Raspberry Pi - but I don’t know a good reason why you could not extend it to three:
Directly connecting to Optical Pulse Counter with RPi? - #2 by pb66
or there’s this with a Raspberry PiZeroW:
Pulse sensor RPI directly - #3 by borpin
There are 3 connections to the optical sensor. 2 & 5 are +5V & GND respectively, 6 is the output. It is not in fact a pulse, in that there is no control of the shape of the output using (say) a Schmitt trigger.
You’ll need @pb66 's Python script etc (possibly modified - I’ve not looked at it) to do the pulse counting as he describes.