You can indeed, the example script used in the Directly connecting to Optical Pulse Counter with RPi? thread can be used on any Pi and theoretically use any number of unused GPIO’s on the Pi so you could have a dozen or so on a standard Pi, things get squeezed a little when you have an emonBase due to the RFM2Pi occupying or obscuring several of the GPIO pins, and things get a little tougher again with the emonPi as the add-on board occupies (but doesn’t actually use) all of the GPIO pins and the case might need to be drilled or cut to allow the additional wires to pass.
My experience of pulse counting has shown very little difference between optical pulses and S0 pulses once the conns are made, so I believe, you could also use an emonTH connected to the S0 contacts of the elec meter if you so desired, that could run on batteries at the remote meter and possibly reach the emonBase/emonPi and the S0 counting should mean the batteries last longer as there is no LED or additional electronics to drive.