What is ApoCas9 in the CRISPR-Cas9 system?
In general, "apo" is used to indicate an apoenzyme — that is the protein part of an enzyme without essential cofactor(s).  

This is actually defined in the Experimental section of the paper:


  Cas9/Cpf1 without gRNA (ApoCas9/Cpf1)


So, in this case ApoCas9 is Cas9 endonuclease that is not bound to a guide RNA.