Didn't the Encyclopedia only use stuff shown on screen? We are talking about the one by the Okudas, right?
Memory Alpha also includes stuff from TAS, which last time I checked, isn't canon.
Upon reading a few pages I can conclude that most of the content is of stuff that was on screen, and I didn't come across anything that I'd call un-canon. One thing I do find funny is that the additional section of all the content from after the previous edition of the encyclopedia was added at the end instead of being properly inserted in alphabetical order, like they couldn't be bothered or something. There are a few slight errors that I noticed, some of the illustrations were wrong or upside down (they've got a Jem' Hadar battleship the wrong way up), but nothing out of the ordinary for something with this much content.
There is a problem or two with using the encyclopedia for the in game wiki, 1) if we straight copy everything in the encyclopedia then it's plagiarism and technically theft, even citing sources it's still a 1-1 copy and would put us in legal hot water, 2) even ignoring that problem there is a huge amount of information in the encyclopedia, even with a team of people copy-writing it would take weeks to do (accounting for the limited time most people can spare for a hobby between work and family). In the end it comes down to how detailed we need the wiki to be, ideally we only need as much information as the player would reasonably wish to access from within the game. Adding too much would hamper their ability to navigate and search the database, not to mention incur larger storage requirements for either local storage (if the database was copied to the players computer to save on bandwidth) or remote storage (if it wasn't).
To limit this there will need to be guidelines for the basic wiki, which I assume the devs will release in due time, but if I had to make a guess I'd say that the wiki would initially be limited to technical (how technology works in Star Trek), scientific (various phenomena that a starship might encounter and how they've been handled before) and light history sections (a limited retelling of the events of all the series and movies as well as approved speculation on the history that occurred between those time periods and outside the scope of the series/films).
TAS is semi-canon, the episode "Yesteryear" has been considered canon by production staff in the past, as much of the content from the episode has been referenced in future episodes (such as the city of Shi'Kahr or Vulcan's Forge). Furthermore I believe there was a vote a while back on startrek.com about the canon status of TAS, though I'm not sure how it turned out.
Poll