I do believe it is legitimate. I get those updates from time to time as well. I do notice significant changes to my tweetdeck after it updates the program and I don't get any residual slow downs or other changes to my computer.
Here's some information about wyUpdate (wyDay):
http://wyday.com/wyupdate/ (explains what it is)
http://wyday.com/wybuild/help/faq.php (some FAQ's)
EDIT:
Also, since the TweetDeck release notes for v2.0.1 mentions wyUpdate by name, I think we can decisively conclude that it is legitimate software.