Per my Japanese coworker's request I'm gonna answer your questions here.
Wikia just has one server which is ONLY based in the U.S. Are you talking about the PAD game server?
We just launched ja.wikia as a new sub-site under Wikia and all international channels are separate. Zh probably will do the same soon. Since PAD game was originally made in Japan and is very popular there, the JA team decided to build up a new one for JA fans there. The ZH PAD wiki is awesome and cannot be surpassed, but because most content are written in Chinese, it's better to have a different one for Japanese users to make it much clearer and more individual.
If you wish to combine the two wikis, a good and common way is to do the inter-wiki links, as you can see on the bottom of most Wikia sites. However, the ZH Pad puts the link of EN site on the top to be remarkable; you can do the same way for JA PAD wiki too.
Hope I answer your questions. Pls leave me messages for further discussion on ZH community central.