The new version of TweetDeck (0.34) is now available. With this version you can use your own url shortener for example Yourls.
You only have to enter following code to “other service” in the TweetDeck settings:
You can find your signature in your webfrontend on Yourls, if you go to tools and there under Secure passwordless API call.
I have tested it and it works great.
Thank you, TweetDeck!