I think this question is a bit old but we have had it come up again and would like to expand on the issue. Encoder inputs do require some extra resources to run. The nice thing about steppers is that we can run them reliably without using an encoder. That being said encoders offer some security and resilience in a motion control design for any type of motors.
The Raspberry Pi cannot handle many encoder inputs. I think it probably has to work pretty hard to handle one encoder input at medium speeds. Its just not what the Raspberry Pi was designed to do. That being said we are working on a product similar to the SlushEngine that supports encoder inputs and limit switches.