Would anyone advise how I can access library catalogues other than those listed within Endnote X2, please? I am particularly interested in searcing in Japanese ones such as Nacsis or NDL.
You can only connect to library catalogues if the library has made its catalogue available on a Z39.50 server. Even if this is the case, they may restrict access to their own users.
NACSIS apparently has a Z39.50 server. See:
You will have to approach them to have your IP address authorised. Then you will have to edit another EndNote connection file to insert the settings for the NACSIS Z39.50 gateway (unless someone else can supply you with this).
I can’t find any indication that the National Diet Library is using a Z39.50 server, but someone else may have more information on this.