Parenthesis in article titles are usually due to a need to distinguish between two similarly named topics. However in books, context is often clear enough that the parenthesis are superfluous. For example in a book on basketball
Robert Smith (basketball) can be renamed
Robert Smith without confusing the reader. To do this, simply write [[Robert Smith (basketball)|Robert Smith]].
Although this should not happen very often, it is possible that some articles should keep their parenthesis. For these, simply write
:[[Robert Smith (basketball)|Robert Smith (basketball)]]
<!--This Robert Smith can be confused with Robert Smith (baseball), also present in this book -->
This will let editors (and WildBot) know that this is intentional. The comment must be
below the link, if it is on the same line, the PDF will ignore the article.