Those sound like typical problems with external links on Wikipedia, not anything specific to Wikia. It's a shame that there isn't an easy way to only see the links in the article namespace, though, as that might make this list of links somewhat more useful (and a lot smaller)...
Is this what you're looking for?
http://en.wikipedia.org/w/index.php?title=Special:Search&ns0=1&redir...
Here is a wonderful example: an article with 39 in-text links to http://piratesonline.wikia.com
http://en.wikipedia.org/w/index.php?title=Pirates_of_the_Caribbean_Online&am...
A.